Alignments for a candidate for acs in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Maridesulfovibrio zosterae DSM 11974

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_027720711.1 H589_RS0103275 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_000425265.1:WP_027720711.1
          Length = 658

 Score =  694 bits (1791), Expect = 0.0
 Identities = 331/650 (50%), Positives = 457/650 (70%), Gaps = 9/650 (1%)

Query: 1   MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGK-ILDWITPYQKVKNTS 59
           M++   +  PA++ ++  ++ ++Y+  Y+++ N+P+ FW E+ + +L W   +  +  + 
Sbjct: 10  MTEQRTYDPPADMQEQACVDIKEYDEIYRRAANEPEAFWAERARELLHWQRDFSSILESD 69

Query: 60  FAPGNVSIKWYEDGTLNLAANCLDRHLQENG-DRTAIIWEGDDTSQSKHISYRELHRDVC 118
                   KW+  G +N + NCLDRHL++   ++ A+IW+G+        +Y  LHR+VC
Sbjct: 70  SEKNEY--KWFGGGRINASYNCLDRHLEQGRRNKAALIWQGEPEEDVSVYTYHMLHREVC 127

Query: 119 RFANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDS 178
           RFAN L  +GI KGD +A+Y+P VPE  +AMLACARIGAVHSV+F GFS  ++  RI+D 
Sbjct: 128 RFANVLKKMGISKGDRIALYLPSVPELVIAMLACARIGAVHSVVFAGFSAVSLKNRILDC 187

Query: 179 SSRLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWR 238
           +++++ITAD  +R G+ IPLK+NVD+AL      SVE VI++KR G DI++ EGRD WW 
Sbjct: 188 NAKILITADGVLRGGKIIPLKRNVDEALFE--CPSVEQVIIVKRAGIDIEFIEGRDTWWH 245

Query: 239 DLIEKASPEH--QPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYH 296
           D I     E   +P  + ++DPLFIL+TSGSTGKPKG++HT GGY+   A T ++VFD  
Sbjct: 246 DEIAALDIEDFCKPVFLKSDDPLFILHTSGSTGKPKGIVHTVGGYMTITAHTMQWVFDIK 305

Query: 297 PGDIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYT 356
             D++WCTAD+GW+TGHSY++YGPL  GATTLMFEGVP +P P R   +V K+ V+I YT
Sbjct: 306 DDDVHWCTADLGWITGHSYVVYGPLESGATTLMFEGVPTYPRPDRYWDIVTKYGVSIFYT 365

Query: 357 APTAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQT 416
           APT IR LM EG +  +  D  SLRILGSVGE INPE W W+ K +GK + P++DTWWQT
Sbjct: 366 APTVIRTLMREGSQWTDKYDLPSLRILGSVGETINPEVWIWFHKHVGKNQLPLLDTWWQT 425

Query: 417 ETGGFMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQART 476
           ETGG +I+PLP   +LK GS  +P  G++ ++V ++G P +    G+LVI + WPG   +
Sbjct: 426 ETGGILISPLPYVDKLKPGSTVKPLPGIEASVVRSDGSPADINEGGHLVINNPWPGMLNS 485

Query: 477 LFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESAL 536
           +  D  R+ +TYF  F   Y +GDGAR DEDG++WI GR+DDV+NVSGHRLGT+EIESAL
Sbjct: 486 IHNDQARYNKTYFERFPGKYETGDGARIDEDGFFWIMGRLDDVINVSGHRLGTSEIESAL 545

Query: 537 VAHPKIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVL 596
           +AHP++ EAAVVGIPH IKGQ+IYAYVTL  G +   ++   +R WV KEIGP+A PD +
Sbjct: 546 IAHPEVTEAAVVGIPHEIKGQSIYAYVTLRPGIDEDDDMRNRLREWVGKEIGPIAVPDTI 605

Query: 597 HWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
            +++ LPKTRSGKIMRRILR+IA GD  + GDTSTL+D  V+  L+E K+
Sbjct: 606 QFSEGLPKTRSGKIMRRILRQIATGD-DHFGDTSTLSDASVITDLIEGKE 654


Lambda     K      H
   0.317    0.135    0.423 

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: 1380
Number of extensions: 71
Number of successful extensions: 6
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: 652
Length of database: 658
Length adjustment: 38
Effective length of query: 614
Effective length of database: 620
Effective search space:   380680
Effective search space used:   380680
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_027720711.1 H589_RS0103275 (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.3699108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.6e-292  954.8   0.0   1.1e-291  954.5   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027720711.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027720711.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  954.5   0.0  1.1e-291  1.1e-291       3     628 ..      29     651 ..      27     652 .. 0.98

  Alignments for each domain:
  == domain 1  score: 954.5 bits;  conditional E-value: 1.1e-291
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvek.rkdk 73 
                                           +++ey e+y++a+++pe+fwa+ a+e l+w+++f+++l+++ e+ ++kWf +g++n+sync+drh+e+ r++k
  NCBI__GCF_000425265.1:WP_027720711.1  29 DIKEYDEIYRRAANEPEAFWAERARELLHWQRDFSSILESDSEKnEYKWFGGGRINASYNCLDRHLEQgRRNK 101
                                           6899**********************************9988777**************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +a+iw g+ ++ed+  +tY+ l+revcr+anvlk++G+ kgdr+a+Ylp +pe+viamlacaRiGavhsvvfa
  NCBI__GCF_000425265.1:WP_027720711.1 102 AALIWQGE-PEEDVSVYTYHMLHREVCRFANVLKKMGISKGDRIALYLPSVPELVIAMLACARIGAVHSVVFA 173
                                           ********.6668************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfsa +l++Ri d++ak++itad+ lRggk+i+lk++vdeal +++ sve+v++vkr+g +++ + egrD+ww
  NCBI__GCF_000425265.1:WP_027720711.1 174 GFSAVSLKNRILDCNAKILITADGVLRGGKIIPLKRNVDEALFECP-SVEQVIIVKRAGIDIE-FIEGRDTWW 244
                                           *********************************************9.7*************76.********* PP

                             TIGR02188 220 eelvek.easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           +++++  + ++ c+p  l+s+dplfiL+tsGstGkPkG++ht+gGy++ +a t+++vfdikd+d++wCtaD+G
  NCBI__GCF_000425265.1:WP_027720711.1 245 HDEIAAlDIEDFCKPVFLKSDDPLFILHTSGSTGKPKGIVHTVGGYMTITAHTMQWVFDIKDDDVHWCTADLG 317
                                           ***9998899*************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           W+tGhsY+vygPL  Gattl+fegvptyp ++r+w+++ ky+v+ifYtaPt+iR+lm++g+++++k+dl slr
  NCBI__GCF_000425265.1:WP_027720711.1 318 WITGHSYVVYGPLESGATTLMFEGVPTYPRPDRYWDIVTKYGVSIFYTAPTVIRTLMREGSQWTDKYDLPSLR 390
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lgsvGe inpe w W++++vGk++ p+ dtwWqtetGgili+plp  + +lkpgs+ +Pl+Giea+vv ++g
  NCBI__GCF_000425265.1:WP_027720711.1 391 ILGSVGETINPEVWIWFHKHVGKNQLPLLDTWWQTETGGILISPLPY-VDKLKPGSTVKPLPGIEASVVRSDG 462
                                           ***********************************************.5************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           ++++ +e+ g Lvi++pwP+ml +i++d+ r+ +tYf++++g y tGDgar d+dG++wi+GR+DdvinvsGh
  NCBI__GCF_000425265.1:WP_027720711.1 463 SPADINEG-GHLVINNPWPGMLNSIHNDQARYNKTYFERFPGKYETGDGARIDEDGFFWIMGRLDDVINVSGH 534
                                           ****9999.8*************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           rlgt+eiesal++h++v+eaavvg+p+eikg++i+a+v+l+ g++ed++ +++ l+++v keigpia pd+i+
  NCBI__GCF_000425265.1:WP_027720711.1 535 RLGTSEIESALIAHPEVTEAAVVGIPHEIKGQSIYAYVTLRPGIDEDDD-MRNRLREWVGKEIGPIAVPDTIQ 606
                                           *********************************************9995.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           + e lPktRsGkimRR+lr+ia+g+++ gd+stl+d sv+ +l+e
  NCBI__GCF_000425265.1:WP_027720711.1 607 FSEGLPKTRSGKIMRRILRQIATGDDHFGDTSTLSDASVITDLIE 651
                                           ****************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (658 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 29.02
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources