Alignments for a candidate for acs in Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 2629598430 Ga0074568_11495 acetyl-coenzyme A synthetase

Query= SwissProt::P31638
         (660 letters)



>IMG__TrieryIMS101_FD:2629598430
          Length = 655

 Score =  730 bits (1884), Expect = 0.0
 Identities = 361/657 (54%), Positives = 472/657 (71%), Gaps = 13/657 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IES++QE R+F PPE F   A I  +E Y+ L ++A+ + E FWA  A   L W + + K
Sbjct: 6   IESILQEKRLFQPPEKFVQTAQIKGIEQYKELYEKAKSNPEEFWAELAETELDWFQKWDK 65

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VL+    PF KWF +G++N SYNCLDR+L     +K A+++E + G    +TY +LH +V
Sbjct: 66  VLEWQ-PPFAKWFINGKINISYNCLDRHLTTWRRNKAALIWEGEPGDSRTITYAQLHREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
           C+ AN  K LG++KGDRV IYMPM  E  +AM ACAR+GA H+VVFGGFSA +L+ RLVD
Sbjct: 125 CQMANVFKQLGVKKGDRVGIYMPMIPEAAIAMLACARIGAPHTVVFGGFSADALKNRLVD 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A  ++TAD   R    +PLK   D AL + G  +V NV+V +RT  K+    GRD W 
Sbjct: 185 AEAKLVVTADGGWRKDAIVPLKEQVDKAL-MAGAPSVENVLVVKRTAQKIQMEPGRDHWW 243

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            D+       C AEP+ +E  LF+LYTSG+TG PKGV H+TGGY L+  +T KW FD++ 
Sbjct: 244 HDLQKSASGECPAEPMDSEDMLFILYTSGTTGTPKGVVHTTGGYNLYTHVTNKWAFDLQD 303

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
            D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P   N G  WD++ ++ V+IFYTA
Sbjct: 304 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCLWDVVEKYGVTIFYTA 363

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTAIR+L+K  E     HP   +L+SLRLLGTVGEPINPEAW+WY++ IG+ +CPIVDT+
Sbjct: 364 PTAIRALMKMGEQ----HPNSRNLTSLRLLGTVGEPINPEAWIWYHRVIGDSKCPIVDTW 419

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
           WQTETGG MITPLPGATP  PGS T P PGI+A IV+E G  V   NGG LVVK PWP M
Sbjct: 420 WQTETGGFMITPLPGATPTKPGSATFPFPGIIADIVNEEGESVDGNNGGYLVVKHPWPGM 479

Query: 484 IRTIWGDPERFRKSYFP---EELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           +RT++GDP+RFR++Y+     + G  +Y AGDG+ +D+D GYF +MGR+DDV+NV+GHR+
Sbjct: 480 MRTVYGDPDRFRRTYWEYLRPKNGEYIYFAGDGAHKDED-GYFWVMGRVDDVINVAGHRL 538

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTME+ESALVS+P VAEAAVVG+PD++ GE I AFV L+  R   E   K   EL+  V 
Sbjct: 539 GTMEVESALVSHPAVAEAAVVGKPDEVKGEDIVAFVSLEGGREPDENLEK---ELKQHVV 595

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
           KEIG IA+P +IRF D+LPKTRSGKIMRRLLRSLA G+EIT DTSTL++ ++L++L+
Sbjct: 596 KEIGAIARPGEIRFTDDLPKTRSGKIMRRLLRSLAAGQEITGDTSTLQDRSVLDKLR 652


Lambda     K      H
   0.319    0.136    0.422 

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: 1419
Number of extensions: 73
Number of successful extensions: 7
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: 660
Length of database: 655
Length adjustment: 38
Effective length of query: 622
Effective length of database: 617
Effective search space:   383774
Effective search space used:   383774
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 2629598430 Ga0074568_11495 (acetyl-coenzyme A synthetase)
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.588461.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 1019.2   0.0          0 1019.0   0.0    1.0  1  IMG__TrieryIMS101_FD:2629598430  


Domain annotation for each sequence (and alignments):
>> IMG__TrieryIMS101_FD:2629598430  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1019.0   0.0         0         0       2     627 ..      29     652 ..      28     654 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1019.0 bits;  conditional E-value: 0
                        TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiw 78 
                                      + +e+ykelye+a+++pe+fwa+la++el+w+++++kvl+++ +p++kWf +g++n+sync+drh+++ r++k+a+iw
  IMG__TrieryIMS101_FD:2629598430  29 KGIEQYKELYEKAKSNPEEFWAELAETELDWFQKWDKVLEWQ-PPFAKWFINGKINISYNCLDRHLTTwRRNKAALIW 105
                                      6789*************************************9.89********************************* PP

                        TIGR02188  79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeR 156
                                      eg+ +g dsr++tYa+l+revc++anv+k+lGvkkgdrv iY+pmipea+iamlacaRiGa h+vvf+Gfsa+al++R
  IMG__TrieryIMS101_FD:2629598430 106 EGE-PG-DSRTITYAQLHREVCQMANVFKQLGVKKGDRVGIYMPMIPEAAIAMLACARIGAPHTVVFGGFSADALKNR 181
                                      ***.77.59********************************************************************* PP

                        TIGR02188 157 ivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekeasaecepe 234
                                      +vdaeaklv+tad+g+R++ +++lk++vd+al +   sve+vlvvkrt ++++ ++ grD+ww++l ++ as ec++e
  IMG__TrieryIMS101_FD:2629598430 182 LVDAEAKLVVTADGGWRKDAIVPLKEQVDKALMAGAPSVENVLVVKRTAQKIQ-MEPGRDHWWHDLQKS-ASGECPAE 257
                                      *********************************9999**************76.**************5.******** PP

                        TIGR02188 235 kldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattll 312
                                      ++dsed+lfiLYtsG+tG+PkGv+httgGy l++++t k+ fd++d+d++wCtaDvGW+tGhsYivygPL+nGattl+
  IMG__TrieryIMS101_FD:2629598430 258 PMDSEDMLFILYTSGTTGTPKGVVHTTGGYNLYTHVTNKWAFDLQDTDVYWCTADVGWITGHSYIVYGPLSNGATTLM 335
                                      ****************************************************************************** PP

                        TIGR02188 313 fegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekc 390
                                      +eg+p+ ++++++w+v+eky+vtifYtaPtaiRalmk+ge+++++++l slr+lg+vGepinpeaw Wy++v+G++kc
  IMG__TrieryIMS101_FD:2629598430 336 YEGAPRASNPGCLWDVVEKYGVTIFYTAPTAIRALMKMGEQHPNSRNLTSLRLLGTVGEPINPEAWIWYHRVIGDSKC 413
                                      ****************************************************************************** PP

                        TIGR02188 391 pivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeer 468
                                      pivdtwWqtetGg++itplpg at++kpgsat P++Gi a++v+eeg++v+ +++ g+Lv+k+pwP+m+rt+ygd++r
  IMG__TrieryIMS101_FD:2629598430 414 PIVDTWWQTETGGFMITPLPG-ATPTKPGSATFPFPGIIADIVNEEGESVDGNNG-GYLVVKHPWPGMMRTVYGDPDR 489
                                      *********************.6****************************9888.8********************* PP

                        TIGR02188 469 fvetYfkklkg.....lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikg 541
                                      f +tY++ l+      +yf+GDga++d+dGy+w++GRvDdvinv+Ghrlgt+e+esalvsh+avaeaavvg+pde+kg
  IMG__TrieryIMS101_FD:2629598430 490 FRRTYWEYLRPkngeyIYFAGDGAHKDEDGYFWVMGRVDDVINVAGHRLGTMEVESALVSHPAVAEAAVVGKPDEVKG 567
                                      ******98766678889************************************************************* PP

                        TIGR02188 542 eaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstled 619
                                      e ivafv l+ g+e+de+ lekelk++v keig+ia+p +i+++++lPktRsGkimRRllr++a+g+e++gd+stl+d
  IMG__TrieryIMS101_FD:2629598430 568 EDIVAFVSLEGGREPDEN-LEKELKQHVVKEIGAIARPGEIRFTDDLPKTRSGKIMRRLLRSLAAGQEITGDTSTLQD 644
                                      *****************5.*********************************************************** PP

                        TIGR02188 620 psvveelk 627
                                      +sv+++l+
  IMG__TrieryIMS101_FD:2629598430 645 RSVLDKLR 652
                                      *****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (655 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: 26.64
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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