Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_010961287.1 MCA_RS10000 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>NCBI__GCF_000008325.1:WP_010961287.1
Length = 662
Score = 837 bits (2161), Expect = 0.0
Identities = 402/643 (62%), Positives = 490/643 (76%), Gaps = 5/643 (0%)
Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59
M +YPV ++A S + Y+ MY +S+ +P+GFW E A+ + W P+ V + +
Sbjct: 19 MKTEHVYPVPSDIATSARITDEIYREMYDRSIRDPEGFWAELAQEFISWNTPWQRVARWN 78
Query: 60 FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCK 119
F H I+WF+ LNVSYNCLDRHLA+R DQ AI+WEGD+P + R +TY ELH+ VC+
Sbjct: 79 F--HTPSIEWFSGARLNVSYNCLDRHLADRRDQTAILWEGDEPGDQRALTYGELHDRVCR 136
Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179
FAN L+ V +GD V IY+PMIPEA VAMLAC RIGAIHS+VFGGFS EAL RI+D
Sbjct: 137 FANVLKSHGVGKGDRVCIYLPMIPEAAVAMLACARIGAIHSIVFGGFSSEALKDRILDAD 196
Query: 180 SKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYED 239
+V+I ADEG R GK +PLK NVD AL+ + ++ V+V + T + W RD W+ +
Sbjct: 197 CRVLICADEGRRGGKFVPLKRNVDAALS--QCPHVETVLVVRHTGRPVDWTAGRDHWFHE 254
Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGE 299
++ A C P++M AE+ LFILYTSGSTGKPKGV HTT GYLL+AA+TH+ VFDY+ GE
Sbjct: 255 AVQSASADCPPEDMDAEDPLFILYTSGSTGKPKGVVHTTGGYLLFAAVTHKYVFDYRDGE 314
Query: 300 VYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPT 359
VYWCTAD+GW+TGHSY+V+GPL NGATTL+FEGVP YP R+ ++IDK++VSI YTAPT
Sbjct: 315 VYWCTADIGWITGHSYVVFGPLCNGATTLMFEGVPTYPTPARLWQIIDKYQVSIFYTAPT 374
Query: 360 AIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETG 419
IRA+M G V+ AD SLR+LGSVGEPINPEAW+WYY+ VG++RCP++DTWWQTETG
Sbjct: 375 VIRALMGLGADWVKQADRHSLRILGSVGEPINPEAWEWYYQEVGEKRCPVLDTWWQTETG 434
Query: 420 GVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYG 479
G++I+PLPGAT LKPGSATRPFFGVVP ++D GN + G AEG L I SWPGQART++
Sbjct: 435 GIMITPLPGATPLKPGSATRPFFGVVPVILDPQGNELTGPAEGVLAIAASWPGQARTVFR 494
Query: 480 DHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
+HDRF +TYF + G YFTGDGARRD DGYYWITGRVDDV+NVSGHRMGTAEIESA+V H
Sbjct: 495 NHDRFRETYFALYPGKYFTGDGARRDADGYYWITGRVDDVINVSGHRMGTAEIESALVLH 554
Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWA 599
VAEAAVVG PH+IKGQGIY YVTL A SE L+ +L VR+EIG IA+PD+IQW
Sbjct: 555 DSVAEAAVVGYPHNIKGQGIYAYVTLVADAVPSEDLKRQLIELVREEIGAIATPDIIQWT 614
Query: 600 PGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
P LPKTRSGKIMRRILRKIA E D LGD STLADP VV +I
Sbjct: 615 PALPKTRSGKIMRRILRKIAANELDQLGDTSTLADPAVVEDII 657
Lambda K H
0.318 0.135 0.418
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: 1388
Number of extensions: 69
Number of successful extensions: 3
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: 662
Length adjustment: 38
Effective length of query: 613
Effective length of database: 624
Effective search space: 382512
Effective search space used: 382512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate WP_010961287.1 MCA_RS10000 (acetate--CoA ligase)
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.25852.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 1030.1 0.0 0 1029.8 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961287.1 MCA_RS10000 acetate--CoA ligase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010961287.1 MCA_RS10000 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1029.8 0.0 0 0 5 628 .. 40 658 .. 36 659 .. 0.99
Alignments for each domain:
== domain 1 score: 1029.8 bits; conditional E-value: 0
TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkd 72
e y+e+y+++i+dpe fwa+la+e ++w +p+++v ++++++ +++Wf++++lnvsync+drh+++r+d
lcl|NCBI__GCF_000008325.1:WP_010961287.1 40 EIYREMYDRSIRDPEGFWAELAQEFISWNTPWQRVARWNFHTpSIEWFSGARLNVSYNCLDRHLADRRD 108
679*************************************988************************** PP
TIGR02188 73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavh 141
++ai wegde+g+ +r+ltY el+++vcr+anvlk++Gv kgdrv+iYlpmipea++amlacaRiGa+h
lcl|NCBI__GCF_000008325.1:WP_010961287.1 109 QTAILWEGDEPGD-QRALTYGELHDRVCRFANVLKSHGVGKGDRVCIYLPMIPEAAVAMLACARIGAIH 176
***********95.******************************************************* PP
TIGR02188 142 svvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevae 210
s+vf+Gfs+eal++Ri da+++++i+adeg Rggk ++lk++vd+al++++ +ve+vlvv++tg++v
lcl|NCBI__GCF_000008325.1:WP_010961287.1 177 SIVFGGFSSEALKDRILDADCRVLICADEGRRGGKFVPLKRNVDAALSQCP-HVETVLVVRHTGRPVD- 243
**************************************************9.7*************66. PP
TIGR02188 211 wkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279
w+ grD+w++e+v++ asa+c+pe++d+edplfiLYtsGstGkPkGv+httgGyll aa+t+kyvfd++
lcl|NCBI__GCF_000008325.1:WP_010961287.1 244 WTAGRDHWFHEAVQS-ASADCPPEDMDAEDPLFILYTSGSTGKPKGVVHTTGGYLLFAAVTHKYVFDYR 311
**************6.***************************************************** PP
TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalm 348
d++++wCtaD+GW+tGhsY+v+gPL+nGattl+fegvptyp+++r+w++i+ky+v+ifYtaPt+iRalm
lcl|NCBI__GCF_000008325.1:WP_010961287.1 312 DGEVYWCTADIGWITGHSYVVFGPLCNGATTLMFEGVPTYPTPARLWQIIDKYQVSIFYTAPTVIRALM 380
********************************************************************* PP
TIGR02188 349 klgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelk 417
lg ++vk+ d++slr+lgsvGepinpeaweWyy++vG+++cp+ dtwWqtetGgi+itplpg at+lk
lcl|NCBI__GCF_000008325.1:WP_010961287.1 381 GLGADWVKQADRHSLRILGSVGEPINPEAWEWYYQEVGEKRCPVLDTWWQTETGGIMITPLPG-ATPLK 448
***************************************************************.6**** PP
TIGR02188 418 pgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDg 486
pgsat+P+fG+ ++++d +g+e++ +e gvL+i +wP+++rt++++++rf etYf ++g yftGDg
lcl|NCBI__GCF_000008325.1:WP_010961287.1 449 PGSATRPFFGVVPVILDPQGNELTGPAE-GVLAIAASWPGQARTVFRNHDRFRETYFALYPGKYFTGDG 516
************************8888.8*************************************** PP
TIGR02188 487 arrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegve 555
arrd+dGy+wi+GRvDdvinvsGhr+gtaeiesalv h++vaeaavvg+p++ikg+ i+a+v+l + +
lcl|NCBI__GCF_000008325.1:WP_010961287.1 517 ARRDADGYYWITGRVDDVINVSGHRMGTAEIESALVLHDSVAEAAVVGYPHNIKGQGIYAYVTLVADAV 585
********************************************************************* PP
TIGR02188 556 edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvv 623
++e+ l+++l++lvr+eig+ia+pd i+++++lPktRsGkimRR+lrkia++e ++lgd+stl+dp+vv
lcl|NCBI__GCF_000008325.1:WP_010961287.1 586 PSED-LKRQLIELVREEIGAIATPDIIQWTPALPKTRSGKIMRRILRKIAANElDQLGDTSTLADPAVV 653
9995.**************************************************************** PP
TIGR02188 624 eelke 628
e++++
lcl|NCBI__GCF_000008325.1:WP_010961287.1 654 EDIIR 658
*9986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (662 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 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 8.00
//
[ok]
This GapMind analysis is from Sep 24 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