Alignments for a candidate for acs in Aquimarina agarilytica ZC1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Aquimarina agarilytica ZC1

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_010182874.1 KQA_RS0217390 acetate--CoA ligase

Query= BRENDA::Q9NR19
         (701 letters)



>NCBI__GCF_000255455.1:WP_010182874.1
          Length = 639

 Score =  659 bits (1700), Expect = 0.0
 Identities = 345/664 (51%), Positives = 434/664 (65%), Gaps = 38/664 (5%)

Query: 34  EVSRSAHVPSLQRYRELHRRSVEEPREFWGDIAKEFYWKTPCPGPFLRYNFDVTKGKIFI 93
           E+  +  V S   Y++ +++SV  P EFW  IA +FYW+       L Y+F++ K    +
Sbjct: 2   EIPNNLQVKSFAEYKQWYQKSVTHPEEFWEAIAGKFYWRKKWETT-LEYDFNIPK----V 56

Query: 94  EWMKGATTNICYNVLDRNVHEKKLGDKVAFYWEGNEPGETTQ-ITYHQLLVQVCQFSNVL 152
           EW KG   NI  N LDR  H K +G+K A  WE N+P E T+ ITY QL V+V  F+NVL
Sbjct: 57  EWFKGGKLNITENCLDR--HLKTIGNKTAIIWEPNDPDEETRHITYRQLYVKVSHFANVL 114

Query: 153 RKQGIQKGDRVAIYMPMIPELVVAMLACARIGALHSIVFAGFSSESLCERILDSSCSLLI 212
           +  GI+KGDRV IYMPMIPEL +AMLACARIGA+HSIVFAGFSS ++  RI D+ C +LI
Sbjct: 115 KNNGIKKGDRVCIYMPMIPELAIAMLACARIGAIHSIVFAGFSSTAIASRINDAGCKMLI 174

Query: 213 TTDAFYRGEKLVNLKELADEALQKCQEKGFPVRCCIVVKHLGRAELGMGDSTSQSPPIKR 272
           T +  YRG K V LK + DEALQ           CI    + R        T +  P+K 
Sbjct: 175 TANEVYRGTKPVALKSICDEALQHTP--------CIETVIVYRR-------TVEPTPMK- 218

Query: 273 SCPDVQISWNQGIDLWWHELMQEAGDECEPEWCDAEDPLFILYTSGSTGKPKGVVHTVGG 332
                      G D +W + +Q+   ECE E  DAED LFILYTSGSTGKPKG+VHT GG
Sbjct: 219 ----------PGRDKFWFDELQKVAKECEAEEMDAEDELFILYTSGSTGKPKGMVHTTGG 268

Query: 333 YMLYVATTFKYVFDFHAEDVFWCTADIGWITGHSYVTYGPLANGATSVLFEGIPTYPDVN 392
           YM+    +F+ VF   A DV+WCTADIGWITGHSY+ YGPLA GAT+V+FEG+P+YPD  
Sbjct: 269 YMVGSTFSFQNVFQLGANDVYWCTADIGWITGHSYIIYGPLAAGATTVMFEGVPSYPDYG 328

Query: 393 RLWSIVDKYKVTKFYTAPTAIRLLMKFGDEPVTKHSRASLQVLGTVGEPINPEAWLWYHR 452
           R W I +K KVT FYTAPTAIR L K   + V KH  +SL+VLG+VGEPIN EAW WY+ 
Sbjct: 329 RFWEICNKLKVTHFYTAPTAIRALAKQSLDFVKKHDLSSLKVLGSVGEPINEEAWHWYND 388

Query: 453 VVGAQRCPIVDTFWQTETGGHMLTPLPGATPMKPGSATFPFFGVAPAILNESGEEL---E 509
            +G   CPIVDT+WQTETG  M++PL G TP +P  AT P  GV P +++ +GE +    
Sbjct: 389 HIGKGNCPIVDTWWQTETGAIMISPLAGITPTRPTFATLPLPGVQPVLMDANGEPIPLKP 448

Query: 510 GEAEGYLVFKQPWPGIMRTVYGNHERFETTYFKKFPGYYVTGDGCQRDQDGYYWITGRID 569
            ++EG L  + PWP + RTVYGNHER++  YF +FPG Y TGDG  RD  G Y ITGR+D
Sbjct: 449 QQSEGRLAIQFPWPSMARTVYGNHERYKQVYFSQFPGNYFTGDGAYRDASGNYRITGRVD 508

Query: 570 DMLNVSGHLLSTAEVESALVEHEAVAEAAVVGHPHPVKGECLYCFVTLCDGHTFSPKLTE 629
           D++ VSGH L TA +E+++ EH AVAE+A+VG PH +KG  L  +VTL D +  S  L  
Sbjct: 509 DVVIVSGHNLGTAPIENSINEHMAVAESAIVGFPHEIKGTALCAYVTLHDNYKASSDLIN 568

Query: 630 ELKKQIREKIGPIATPDYIQNAPGLPKTRSGKIMRRVLRKIAQNDHD-LGDMSTVADPSV 688
           E+K QI   IG IA PD +     LPKTRSGKIMRR+LRKIA N+ D LGD ST+ +P  
Sbjct: 569 EIKIQIANTIGAIAKPDIVVFVNALPKTRSGKIMRRILRKIASNETDSLGDTSTLLNPDA 628

Query: 689 ISHL 692
           +  +
Sbjct: 629 VEQI 632


Lambda     K      H
   0.320    0.138    0.440 

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: 1250
Number of extensions: 51
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: 701
Length of database: 639
Length adjustment: 39
Effective length of query: 662
Effective length of database: 600
Effective search space:   397200
Effective search space used:   397200
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 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_010182874.1 KQA_RS0217390 (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.3123193.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-284  930.8   0.1   1.9e-284  930.6   0.1    1.0  1  NCBI__GCF_000255455.1:WP_010182874.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000255455.1:WP_010182874.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  930.6   0.1  1.9e-284  1.9e-284       2     627 ..      10     633 ..       9     635 .. 0.98

  Alignments for each domain:
  == domain 1  score: 930.6 bits;  conditional E-value: 1.9e-284
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++  eyk++y++++++pe+fw+  a  ++ w k++e++l+ +++  kv+Wf++g+ln++ nc+drh+++  +k
  NCBI__GCF_000255455.1:WP_010182874.1  10 KSFAEYKQWYQKSVTHPEEFWEAIAG-KFYWRKKWETTLEYDFNIpKVEWFKGGKLNITENCLDRHLKTIGNK 81 
                                           57789********************9.5**************9988*************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwe ++++e++r++tY++l+ +v+++anvlk+ G+kkgdrv+iY+pmipe++iamlacaRiGa+hs+vfa
  NCBI__GCF_000255455.1:WP_010182874.1  82 TAIIWEPNDPDEETRHITYRQLYVKVSHFANVLKNNGIKKGDRVCIYMPMIPELAIAMLACARIGAIHSIVFA 154
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs+ a+a+Ri+da +k++ita+e +Rg k ++lk+i deal+++++ +e+v+v++rt e+ +++k grD+ w
  NCBI__GCF_000255455.1:WP_010182874.1 155 GFSSTAIASRINDAGCKMLITANEVYRGTKPVALKSICDEALQHTPC-IETVIVYRRTVEP-TPMKPGRDKFW 225
                                           *********************************************95.*************.66*******99 PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                            ++++k + +ece+e++d+ed lfiLYtsGstGkPkG++httgGy++  + +++ vf++  +d++wCtaD+GW
  NCBI__GCF_000255455.1:WP_010182874.1 226 FDELQK-VAKECEAEEMDAEDELFILYTSGSTGKPKGMVHTTGGYMVGSTFSFQNVFQLGANDVYWCTADIGW 297
                                           999996.9***************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           +tGhsYi+ygPLa+Gatt++fegvp+ypd +rfwe+++k kvt+fYtaPtaiRal k++ ++vkkhdlssl+v
  NCBI__GCF_000255455.1:WP_010182874.1 298 ITGHSYIIYGPLAAGATTVMFEGVPSYPDYGRFWEICNKLKVTHFYTAPTAIRALAKQSLDFVKKHDLSSLKV 370
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lgsvGepin eaw+Wy++++Gk++cpivdtwWqtetG+i+i+pl+g +t+++p  atlPl+G++++++d +g+
  NCBI__GCF_000255455.1:WP_010182874.1 371 LGSVGEPINEEAWHWYNDHIGKGNCPIVDTWWQTETGAIMISPLAG-ITPTRPTFATLPLPGVQPVLMDANGE 442
                                           **********************************************.5************************* PP

                             TIGR02188 439 eve..eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           ++   +++++g L+i+ pwPsm+rt+yg++er+ ++Yf++++g yftGDga rd+ G + i+GRvDdv+ vsG
  NCBI__GCF_000255455.1:WP_010182874.1 443 PIPlkPQQSEGRLAIQFPWPSMARTVYGNHERYKQVYFSQFPGNYFTGDGAYRDASGNYRITGRVDDVVIVSG 515
                                           9987678888*************************************************************** PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           h+lgta ie+++ +h avae+a+vg+p+eikg a++a+v+l+++++++++ l +e+k +++++ig+iakpd +
  NCBI__GCF_000255455.1:WP_010182874.1 516 HNLGTAPIENSINEHMAVAESAIVGFPHEIKGTALCAYVTLHDNYKASSD-LINEIKIQIANTIGAIAKPDIV 587
                                           ***********************************************995.********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                            +v++lPktRsGkimRR+lrkia++e ++lgd+stl +p +ve+++
  NCBI__GCF_000255455.1:WP_010182874.1 588 VFVNALPKTRSGKIMRRILRKIASNEtDSLGDTSTLLNPDAVEQII 633
                                           **************************99***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (639 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: 29.26
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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