Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo3_N2E3:AO353_03060
(651 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963
Length = 651
Score = 1295 bits (3352), Expect = 0.0
Identities = 623/651 (95%), Positives = 639/651 (98%)
Query: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
MSAASLYPVRPEV ANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1 MSAASLYPVRPEVLANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQ+AIIWEGDDPAESRNITYRELHEQVCKF
Sbjct: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEQVCKF 120
Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDC+S
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRS 180
Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRTGG+IKWNQHRDIW+EDL
Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTGGDIKWNQHRDIWFEDL 240
Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAA+THERVFDYRPGEI
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAAMTHERVFDYRPGEI 300
Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
YWCTADVGWVTGH+YIVYGPLANGATTLLFEGVPNYPDITRVAKI+DKHKVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360
Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
IRAMMA GTAAVEGADGSSLRLLGSVGEPINPEAW+WYYKNVG+SRCPIVDTWWQTETG
Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKSRCPIVDTWWQTETGG 420
Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
+MSPLPGAH LKPGSAARPFFGVVPALVDNLGNI+EG AEGNLVILDSWPGQARTL+GD
Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNIVEGEAEGNLVILDSWPGQARTLFGD 480
Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
HDRFVDTYFKTFRGMYFTGDGARRDADGY+WITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
KVAEAAVVGVPHDIKGQGIYVYVTL GEEP+E LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEQLRLELKNWVRKEIGPIASPDVIQWAP 600
Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
GLPKTRSGKIMRRILRKIAT EY+GLGDISTLADP VVQHLIDTHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYEGLGDISTLADPSVVQHLIDTHKTMNVA 651
Lambda K H
0.319 0.136 0.425
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1747
Number of extensions: 55
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space: 375769
Effective search space used: 375769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate PfGW456L13_1963 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR02188.hmm
# target sequence database: /tmp/gapView.5894.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02188 [M=629]
Accession: TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1023.9 0.1 0 1023.7 0.1 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1023.7 0.1 0 0 3 628 .. 20 643 .. 18 644 .. 0.98
Alignments for each domain:
== domain 1 score: 1023.7 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedg 54
+ +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++ ++kWf+dg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADG 73
5679*********************5.*************99887789******* PP
TIGR02188 55 elnvsyncvdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkel 109
+lnvsync+drh+++r d+vaiiwegd++ e sr++tY+el+++vc++an+l+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 74 TLNVSYNCLDRHLAERGDQVAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQ 127
*****************************96.*********************** PP
TIGR02188 110 GvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdaeakl 164
v++gd v+iY+pmipeav+amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 128 DVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRSKV 182
******************************************************* PP
TIGR02188 165 vitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
vitadeg+R gk+i+lk++vd+al++ e+ s++kv+v+krtg +++ w++ rD+w
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 183 VITADEGIRAGKKIPLKANVDDALTNPETsSIQKVIVCKRTGGDIK-WNQHRDIW 236
**************************9998**************76.******** PP
TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvk 273
+e+l++ a + c+p+++++e+ lfiLYtsGstGkPkGv+httgGyll+aa+t++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 237 FEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAAMTHE 290
******5.*********************************************** PP
TIGR02188 274 yvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwev 328
vfd+++++i+wCtaDvGWvtGhsYivygPLanGattllfegvp+ypd r++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 291 RVFDYRPGEIYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKI 345
******************************************************* PP
TIGR02188 329 iekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyye 383
++k+kv+i+YtaPtaiRa+m+ g+++v+ d sslr+lgsvGepinpeaw+Wyy+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 346 VDKHKVNILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYK 400
******************************************************* PP
TIGR02188 384 vvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
+vGk++cpivdtwWqtetGg +++plpg a +lkpgsa++P+fG+ +++vd+ g+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 401 NVGKSRCPIVDTWWQTETGGNMMSPLPG-AHALKPGSAARPFFGVVPALVDNLGN 454
****************************.6************************* PP
TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdG 493
ve e+e g Lvi ++wP+++rt++gd++rfv+tYfk+++g+yftGDgarrd+dG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 455 IVEGEAE-GNLVILDSWPGQARTLFGDHDRFVDTYFKTFRGMYFTGDGARRDADG 508
***8888.79********************************************* PP
TIGR02188 494 yiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafv 548
y+wi+GRvDdv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 509 YYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYV 563
******************************************************* PP
TIGR02188 549 vlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrk 603
+lk+g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimRR+lrk
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 564 TLKNGEEPNE-QLRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRK 617
*********9.6******************************************* PP
TIGR02188 604 iaege.ellgdvstledpsvveelke 628
ia+ e e lgd+stl+dpsvv++l++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 618 IATAEyEGLGDISTLADPSVVQHLID 643
*****9****************9975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (651 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.38
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory