Alignments for a candidate for acs in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Marinobacter adhaerens HP15

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF832 HP15_811 acetyl-CoA synthetase

Query= SwissProt::Q8ZKF6
         (652 letters)



>FitnessBrowser__Marino:GFF832
          Length = 649

 Score =  968 bits (2502), Expect = 0.0
 Identities = 455/643 (70%), Positives = 535/643 (83%), Gaps = 1/643 (0%)

Query: 1   MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSF 60
           M+    + +   +A + L+N EQYE  Y+QS+ DPDTFWGE GK L+WI PY KVKNT++
Sbjct: 1   MTGKQVYPVSPEVAKQALLNREQYEEMYRQSVEDPDTFWGEHGKRLEWIKPYTKVKNTTY 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRF 120
              N+SIKW+EDG LN +ANCLDRHL++ GD+TAII+EGDD + S++++YRELH +  +F
Sbjct: 61  DYNNLSIKWFEDGQLNASANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELHEETSKF 120

Query: 121 ANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSS 180
           AN L  LG+KKGDVV IYMPM+ E AVAMLACARIGA+HSV+FGGFSPEA+  RI++  S
Sbjct: 121 ANVLKGLGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPEALGARIVNGKS 180

Query: 181 RLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTG-SDIDWQEGRDLWWRD 239
           R V+TADEGVR GR IPLKKNVD ALKN +  +VE V+V+ RTG S++ W E RD  + D
Sbjct: 181 RFVVTADEGVRGGRKIPLKKNVDAALKNEDAANVEKVVVVTRTGNSEVPWNEARDERYED 240

Query: 240 LIEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGD 299
           L++ AS + QPE MNAEDPLF+LYTSGSTG PKGVLHTTGGY+VYA+ T +YVFDYH GD
Sbjct: 241 LMKSASADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGD 300

Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPT 359
           +YWCTAD GWVTGHSY+LYGPLA GA T++FEGVPN+P  +RM QVVDKH+VNILYTAPT
Sbjct: 301 VYWCTADFGWVTGHSYILYGPLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPT 360

Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETG 419
           AIRALMAEG+  + GT R SL++LGSVGEPINPEAWEWY + IG  KCP+VDTWWQTETG
Sbjct: 361 AIRALMAEGESCMNGTTRESLKLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETG 420

Query: 420 GFMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFG 479
           G +I+PLPGAI+LK GSAT PFFGVQPALVDN+G+  EG TEGNLVI DSWPGQ RT++G
Sbjct: 421 GILISPLPGAIDLKPGSATVPFFGVQPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYG 480

Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539
           DHERF QTYFST+K MYF+GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H
Sbjct: 481 DHERFAQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSH 540

Query: 540 PKIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599
            K+AEAAVVG PH IKGQ IY YVTL HG+EPS EL  E+  WVRKEIGP+A+PDV+ W 
Sbjct: 541 EKVAEAAVVGYPHDIKGQGIYVYVTLVHGQEPSDELKKELVQWVRKEIGPIASPDVIQWA 600

Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLL 642
             LPKTRSGKIMRRILRKIAA +   LGDTSTLADPGVV+ L+
Sbjct: 601 PGLPKTRSGKIMRRILRKIAANEHDQLGDTSTLADPGVVDDLI 643


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: 1485
Number of extensions: 64
Number of successful extensions: 2
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: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
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 GFF832 HP15_811 (acetyl-CoA 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.7128.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 1029.2   0.0          0 1029.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF832  HP15_811 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF832  HP15_811 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1029.0   0.0         0         0       3     627 ..      20     643 ..      18     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1029.0 bits;  conditional E-value: 0
                          TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                        + e+y+e+y++++edp++fw++++k +lew+kp++kv++++ +    ++kWfedg+ln+s+nc+drh+ekr d++a
  lcl|FitnessBrowser__Marino:GFF832  20 NREQYEEMYRQSVEDPDTFWGEHGK-RLEWIKPYTKVKNTTYDYnnlSIKWFEDGQLNASANCLDRHLEKRGDQTA 94 
                                        679**********************.5***********9986655579**************************** PP

                          TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                        ii+egd++  dsr++tY+el++e++++anvlk lGvkkgd v+iY+pmi+e+++amlacaRiGa+hsvvf+Gfs+e
  lcl|FitnessBrowser__Marino:GFF832  95 IIFEGDDPA-DSRNVTYRELHEETSKFANVLKGLGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPE 169
                                        ********9.5***************************************************************** PP

                          TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelveke 226
                                        al  Riv+ ++++v+tadeg+Rgg++i+lkk+vd+al+++++ +vekv+vv rtg++ ++w+e rD  +e+l+++ 
  lcl|FitnessBrowser__Marino:GFF832 170 ALGARIVNGKSRFVVTADEGVRGGRKIPLKKNVDAALKNEDAaNVEKVVVVTRTGNSEVPWNEARDERYEDLMKS- 244
                                        ***************************************9999*************99****************6. PP

                          TIGR02188 227 asaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302
                                        asa+c+pe++++edplf+LYtsGstG PkGvlhttgGy+++a++t++yvfd++++d++wCtaD GWvtGhsYi+yg
  lcl|FitnessBrowser__Marino:GFF832 245 ASADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGDVYWCTADFGWVTGHSYILYG 320
                                        **************************************************************************** PP

                          TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaw 378
                                        PLanGa t+lfegvp+ypd+sr+ +v++k+kv+i+YtaPtaiRalm++ge+ ++ + ++sl++lgsvGepinpeaw
  lcl|FitnessBrowser__Marino:GFF832 321 PLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPTAIRALMAEGESCMNGTTRESLKLLGSVGEPINPEAW 396
                                        **************************************************************************** PP

                          TIGR02188 379 eWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkp 454
                                        eWy++v+G++kcpivdtwWqtetGgili+plpg a++lkpgsat+P+fG+++++vd++g+ +e ++e g Lvi ++
  lcl|FitnessBrowser__Marino:GFF832 397 EWYHRVIGNSKCPIVDTWWQTETGGILISPLPG-AIDLKPGSATVPFFGVQPALVDNDGNILEGKTE-GNLVILDS 470
                                        *********************************.6****************************8777.79****** PP

                          TIGR02188 455 wPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaea 530
                                        wP+++rtiygd+erf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsGhrlgtae+esalvshe+vaea
  lcl|FitnessBrowser__Marino:GFF832 471 WPGQMRTIYGDHERFAQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHEKVAEA 546
                                        **************************************************************************** PP

                          TIGR02188 531 avvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606
                                        avvg+p++ikg+ i+++v+l +g+e+++e l+kel ++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+
  lcl|FitnessBrowser__Marino:GFF832 547 AVVGYPHDIKGQGIYVYVTLVHGQEPSDE-LKKELVQWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAA 621
                                        ****************************5.********************************************** PP

                          TIGR02188 607 ge.ellgdvstledpsvveelk 627
                                        +e ++lgd+stl+dp vv++l+
  lcl|FitnessBrowser__Marino:GFF832 622 NEhDQLGDTSTLADPGVVDDLI 643
                                        **9****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 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: 10.31
//
[ok]

This GapMind analysis is from Sep 17 2021. 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)
Organisms (tab-delimited)
SQLite3 databases

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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 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