hmmsearch - search a sequence database with a profile HMM

Web document 5.9. Results of the hmmsearch program of HMMER using a set of bacterial and fungal globins as a query (HMM file 02.hmm) and searching a database of human RefSeq proteins (downloaded from the ftp site linked on the home page of NCBI).

Note that there is only one database match (with an E value of 7.1).

HMMER 2.3.2 (Oct 2003)

Freely distributed under the GNU General Public License (GPL)

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HMM file: 02.hmm [globins_bactfungal_]

Sequence database: human.protein.faa

per-sequence score cutoff: [none]

per-domain score cutoff: [none]

per-sequence Eval cutoff: <= 10

per-domain Eval cutoff: [none]

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Query HMM: globins_bactfungal_

Accession: [none]

Description: [none]

[HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):

Sequence Description Score E-value N

-------- ----------- ----- ------- ---

gi|27436879|ref|NP_775104.1| armadillo repeat con -102.4 7.1 1

Parsed for domains:

Sequence Domain seq-f seq-t hmm-f hmm-t score E-value

-------- ------- ----- ----- ----- ----- ----- -------

gi|27436879|ref|NP_775104.1| 1/1 384 582 .. 1 599 [] -102.4 7.1

Alignments of top-scoring domains:

gi|27436879|ref|NP_775104.1|: domain 1 of 1, from 384 to 582: score -102.4, E = 7.1

*->MtSgnvhttkPLtpeqvqiilnsSSiGPVDNLKiNERPGSHDHSmRS

t+++ ++ i P NL

gi|2743687 384 TTCNP---------ANANAAAEADGIDPLINL--------------- 406

EmSSKNassptlpeaiSRSEGSVYQVKiDRGdspnteGFDFKVNARDLLL

+SSK +++ + +

gi|2743687 407 -LSSKRDGAIANA------------------------------------- 418

LRmSWDiLLREYLTPKELKVFQALLYSNKHiTSTERPYLNTAPDGmiSKT

gi|2743687 - -------------------------------------------------- -

iDPTARPRKTKQRDNDNKVDgtlLteqFYdnmlaadPELepfFnetkqkv

+t Lt nm ++P+

gi|2743687 419 --------------------ATVLT-----NMAMQEPLRL---------- 433

rrqPrilakaLlayakNienlgpLldfvkkiasKHvgLqvKpehYpivGk

Ni+n + + ++ + s

gi|2743687 434 ----------------NIQNHDIMHAIISPLRS----------------- 450

aLletmqellGdaLtlElidAWatAYsnLAnlmItaEadlYaeApWtgFr

An ++ a+

gi|2743687 451 -----------------------------ANTVVQSKAA----------- 460

dFrVtkvqrEcseVkSlYltPvdGkplPepkRGQYLarrvDaePslPgea

La+ +a

gi|2743687 461 -----------------------------------LAVTA--------TA 467

yelvggEasiRempkefYyRisvrkllGLNPAEPGAKAHPglvslhlhgr

++ ++R +r GL +lv+l +

gi|2743687 468 CDV--------------EARTELRNSGGLE----------PLVELLRS-K 492

wdnsgdklkvspPcGdFvyesseflvglLgGgqgyrgrhGHPrLrarHmp

+d+++ +++++ +g+ ++ +

gi|2743687 493 NDEVRKHA---------------SWAVMVCAGDELTAN------------ 515

lgideamrdqWLtcmlsaiEarltpaAg.ravrflhPslrtadsrafgkl

+ ++ l ++E++ + g+r+ +f++ a +kl

gi|2743687 516 ---ELCRLG-----ALDILEEVNVS--GtRKNKFSE--------AAYNKL 547

lm.slkipygqqQVPTNKiPTlklteFtStekkgedydlidaiaprtlda

l ++l ++y q+

gi|2743687 548 LNnNLSLKYSQT-------------------------------------- 559

eDLdlIspeddgyllGprgymtdvadylrnrgveDrvKlelFGptAQQKN

gyl ++++n g D + p+

gi|2743687 560 -----------GYLS---------SSNIINDGFYDYGRI---NPG----- 581

Ceiv<-*

gi|2743687 582 ---T 582

Histogram of all scores:

score obs exp (one = represents 24 sequences)

----- --- ---

<-207 4 -|=

-207 0 0|

-206 1 0|=

-205 0 0|

-204 1 0|=

-203 0 0|

-202 1 0|=

-201 1 0|=

-200 2 0|=

-199 3 0|=

-198 1 0|=

-197 1 0|=

-196 6 0|=

-195 2 0|=

-194 12 0|=

-193 12 0|=

-192 6 0|=

-191 12 0|=

-190 11 0|=

-189 18 0|=

-188 18 0|=

-187 21 0|=

-186 26 0|==

-185 33 0|==

-184 25 0|==

-183 35 0|==

-182 43 0|==

-181 45 0|==

-180 36 0|==

-179 51 0|===

-178 46 0|==

-177 65 0|===

-176 64 0|===

-175 92 0|====

-174 98 0|=====

-173 109 0|=====

-172 105 0|=====

-171 132 0|======

-170 129 0|======

-169 169 0|========

-168 144 0|======

-167 163 0|=======

-166 186 0|========

-165 249 0|===========

-164 218 0|==========

-163 281 0|============

-162 269 0|============

-161 322 0|==============

-160 359 0|===============

-159 420 0|==================

-158 426 0|==================

-157 460 0|====================

-156 512 0|======================

-155 606 0|==========================

-154 606 0|==========================

-153 702 0|==============================

-152 769 3|*================================

-151 853 19|*===================================

-150 838 74|===*===============================

-149 950 210|========*===============================

-148 1031 468|===================*=======================

-147 1069 855|===================================*=========

-146 1185 1330|================================================== *

-145 1127 1819|=============================================== *

-144 1198 2241|================================================== *

-143 1296 2539|====================================================== *

-142 1328 2690|======================================================== *

-141 1399 2698|==========================================================*

-140 1329 2591|======================================================== *

-139 1251 2403|===================================================== *

-138 1302 2166|======================================================= *

-137 1122 1908|=============================================== *

-136 1052 1651|============================================ *

-135 937 1407|======================================== *

-134 918 1186|======================================= *

-133 815 990|================================== *

-132 723 820|=============================== *

-131 656 675|============================*

-130 525 553|====================== *

-129 541 451|==================*====

-128 424 367|===============*==

-127 356 298|============*==

-126 266 241|==========*=

-125 230 195|========*=

-124 183 157|======*=

-123 118 127|=====*

-122 114 102|====*

-121 77 82|===*

-120 100 66|==*==

-119 63 53|==*

-118 43 42|=*

-117 33 34|=*

-116 21 27|=*

-115 18 22|*

-114 15 17|*

-113 8 14|*

-112 12 11|*

-111 7 9|*

-110 1 7|*

-109 2 5|*

-108 0 4|*

-107 2 3|*

-106 1 3|*

-105 0 2|*

-104 1 2|*

-103 1 1|*

% Statistical details of theoretical EVD fit:

mu = -140.9514

lambda = 0.2193

chi-sq statistic = 52071.7383

P(chi-square) = 0

Total sequences searched: 33669

Whole sequence top hits:

tophits_s report:

Total hits: 67

Satisfying E cutoff: 1

Total memory: 21K

Domain top hits:

tophits_s report:

Total hits: 67

Satisfying E cutoff: 67

Total memory: 150K