Alignments for a candidate for acs in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Photobacterium jeanii R-40508

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_068330685.1 A3K86_RS09595 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001650345.1:WP_068330685.1
          Length = 649

 Score = 1036 bits (2679), Expect = 0.0
 Identities = 481/648 (74%), Positives = 562/648 (86%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS++H + +   IAD   I   +Y  MYQQS+  PD FW E G+I+DWIKP+ +VKNTSF
Sbjct: 1   MSEVHVYPVNQAIADNAHITDDKYREMYQQSVINPDGFWREHGQIVDWIKPFSQVKNTSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
             G+VS+KW+EDGTLN++ANCLDRHL   GD+ AIIWEGDD S    ++Y ELH++VC+F
Sbjct: 61  DTGHVSVKWFEDGTLNVSANCLDRHLATRGDQPAIIWEGDDPSDDATLTYNELHQEVCKF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN L   G++KGDVV +YMPMV EAAVAMLAC RIGAVH+++FGGFSPEA+AGRI+DSN+
Sbjct: 121 ANALKSQGVRKGDVVCLYMPMVAEAAVAMLACTRIGAVHTIVFGGFSPEALAGRIVDSNA 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           ++V+T+DEG+RAGR++PLKKNVDDA+ N  VTSVE V+VLKRTG  ++W   RD+WWH+ 
Sbjct: 181 KVVVTADEGIRAGRAVPLKKNVDDAIANDEVTSVEKVMVLKRTGSAVEWDSERDVWWHEA 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
              AS+  + EEM+AEDPLFILYTSGSTGKPKGVLHTTGGYLVYA +TFKYVFDY  GDI
Sbjct: 241 TAVASENCEPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTFKYVFDYQEGDI 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGW+TGHSYL+YGPLA GATTL+FEGVPN+P  +RM++VVDKHQV+ILYTAPTA
Sbjct: 301 YWCTADVGWITGHSYLVYGPLANGATTLLFEGVPNYPNTSRMSEVVDKHQVSILYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRALMA+GD+AI GT RSSLRI+GSVGEPINPEAWEWY + IG+ +CP+VDTWWQTETGG
Sbjct: 361 IRALMAKGDEAISGTSRSSLRIMGSVGEPINPEAWEWYHRTIGDSRCPIVDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
            +ITPLPGAT LK GSATRPFFGVQPALVDN GN L+GATEG+LV+ DSWPGQ RTL+GD
Sbjct: 421 ILITPLPGATALKPGSATRPFFGVQPALVDNMGNILDGATEGNLVMIDSWPGQMRTLWGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           HERFEQTYFSTF+ MYF+GDGARRDEDGYYWITGRVDDVLN+SGHR+GTAEIESALVA  
Sbjct: 481 HERFEQTYFSTFQGMYFTGDGARRDEDGYYWITGRVDDVLNISGHRMGTAEIESALVAFD 540

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAA+VG+PH+IKGQAIYAY+TLN GE PS EL+ EV+ WVRKEIGP+ATPD LHWTD
Sbjct: 541 KIAEAAIVGVPHDIKGQAIYAYITLNDGEVPSAELHKEVKEWVRKEIGPIATPDFLHWTD 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAI 648
           +LPKTRSGKIMRRILRKIA GDT  LGDTSTLADP VV+KL+EEKQ I
Sbjct: 601 ALPKTRSGKIMRRILRKIATGDTGTLGDTSTLADPSVVDKLIEEKQKI 648


Lambda     K      H
   0.317    0.135    0.421 

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: 1568
Number of extensions: 48
Number of successful extensions: 1
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 WP_068330685.1 A3K86_RS09595 (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.4183996.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 1020.7   0.6          0 1020.4   0.6    1.0  1  NCBI__GCF_001650345.1:WP_068330685.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001650345.1:WP_068330685.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1020.4   0.6         0         0       4     628 ..      21     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1020.4 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                            ++y+e+y++++ +p+ fw+++++  ++w+kpf++v+++s+++   +vkWfedg+lnvs+nc+drh+++r d+
  NCBI__GCF_001650345.1:WP_068330685.1  21 DDKYREMYQQSVINPDGFWREHGQ-IVDWIKPFSQVKNTSFDTghvSVKWFEDGTLNVSANCLDRHLATRGDQ 92 
                                           589********************9.6***************998889************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                            aiiwegd+++ d  +ltY+el++evc++an+lk++Gv+kgd v++Y+pm+ ea++amlac+RiGavh++vf+
  NCBI__GCF_001650345.1:WP_068330685.1  93 PAIIWEGDDPS-DDATLTYNELHQEVCKFANALKSQGVRKGDVVCLYMPMVAEAAVAMLACTRIGAVHTIVFG 164
                                           **********9.59*********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs+eala Rivd++ak+v+tadeg+R g++++lkk+vd+a+++ e  svekv+v+krtg+ v+ w+++rDvw
  NCBI__GCF_001650345.1:WP_068330685.1 165 GFSPEALAGRIVDSNAKVVVTADEGIRAGRAVPLKKNVDDAIANDEVtSVEKVMVLKRTGSAVE-WDSERDVW 236
                                           *******************************************99988**************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           w+e+++  as++cepe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t+kyvfd++++di+wCtaDvG
  NCBI__GCF_001650345.1:WP_068330685.1 237 WHEATAV-ASENCEPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTFKYVFDYQEGDIYWCTADVG 308
                                           ******5.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           W+tGhsY+vygPLanGattllfegvp+yp++sr+ ev++k++v+i+YtaPtaiRalm++g+e+++ +++sslr
  NCBI__GCF_001650345.1:WP_068330685.1 309 WITGHSYLVYGPLANGATTLLFEGVPNYPNTSRMSEVVDKHQVSILYTAPTAIRALMAKGDEAISGTSRSSLR 381
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           ++gsvGepinpeaweWy++++G+++cpivdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd+ g
  NCBI__GCF_001650345.1:WP_068330685.1 382 IMGSVGEPINPEAWEWYHRTIGDSRCPIVDTWWQTETGGILITPLPG-ATALKPGSATRPFFGVQPALVDNMG 453
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           + ++  +e g Lv+ ++wP+++rt++gd+erf +tYf++++g+yftGDgarrd+dGy+wi+GRvDdv+n+sGh
  NCBI__GCF_001650345.1:WP_068330685.1 454 NILDGATE-GNLVMIDSWPGQMRTLWGDHERFEQTYFSTFQGMYFTGDGARRDEDGYYWITGRVDDVLNISGH 525
                                           ****8777.79************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtaeiesalv+ +++aeaa+vgvp++ikg+ai+a+++l++g+ +++e l+ke+k++vrkeigpia+pd ++
  NCBI__GCF_001650345.1:WP_068330685.1 526 RMGTAEIESALVAFDKIAEAAIVGVPHDIKGQAIYAYITLNDGEVPSAE-LHKEVKEWVRKEIGPIATPDFLH 597
                                           ***********************************************95.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++++lPktRsGkimRR+lrkia+g+  +lgd+stl+dpsvv++l+e
  NCBI__GCF_001650345.1:WP_068330685.1 598 WTDALPKTRSGKIMRRILRKIATGDtGTLGDTSTLADPSVVDKLIE 643
                                           *************************999***************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.89
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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