GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Psychromonas ingrahamii 37

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011771371.1 PING_RS16055 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_000015285.1:WP_011771371.1
          Length = 649

 Score =  998 bits (2580), Expect = 0.0
 Identities = 465/646 (71%), Positives = 547/646 (84%)

Query: 1   MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSF 60
           MS+ H + +  N+A   L+  E+Y T+Y+ SI+DP  FWGE+GKILDWI PY KVKN+SF
Sbjct: 1   MSEEHIYPVTDNLAKNSLLTNEEYLTQYQASISDPSAFWGEKGKILDWIKPYTKVKNSSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRF 120
             G+VSIKW+EDG LN++ANC+DRHL   GD+ AI+WEGD   + + I+Y++LH+ VC+F
Sbjct: 61  DSGHVSIKWFEDGKLNVSANCIDRHLATKGDQVAILWEGDTADKDEKITYKQLHQRVCQF 120

Query: 121 ANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSS 180
           AN L   G++KGDVV +YMPM PEAAVAMLAC RIGAVHS++FGGFSP+A+AGRI+DSS+
Sbjct: 121 ANVLKSQGVRKGDVVCLYMPMTPEAAVAMLACTRIGAVHSIVFGGFSPDAIAGRIVDSSA 180

Query: 181 RLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDL 240
           ++VITADEG R GR +PLK NVD+AL       V+ VIV K TG +++W  GRDL W  +
Sbjct: 181 KIVITADEGRRGGRVVPLKANVDEALTKDGTDCVKSVIVFKNTGGEVNWVVGRDLDWESV 240

Query: 241 IEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDI 300
               S E +PEAMNAEDPLFILYTSGSTG PKGVLHTTGGYLVYAA TFKYVFDY  GDI
Sbjct: 241 CADESSECEPEAMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYAAMTFKYVFDYQEGDI 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTA 360
           YWCTADVGW+TGH+Y +YGPLA GAT+L+FEGVPN+PTPARM +VVDKH+V+ILYTAPTA
Sbjct: 301 YWCTADVGWITGHTYSVYGPLANGATSLIFEGVPNYPTPARMSEVVDKHKVSILYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGG 420
           IRALMA+GD+AIEGT RSSLRILGSVGEPINPEAWEWY+ KIG E+CP+VDTWWQTETGG
Sbjct: 361 IRALMAKGDQAIEGTHRSSLRILGSVGEPINPEAWEWYYNKIGDERCPIVDTWWQTETGG 420

Query: 421 FMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGD 480
            +I+PLPGA +LK GSATRPFFGVQPA+VD+EG   EG   GNLV+ DSWPGQ RTL+ +
Sbjct: 421 ILISPLPGATDLKPGSATRPFFGVQPAIVDSEGVVLEGEAAGNLVMLDSWPGQMRTLYNN 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           H+RFEQTYFSTFK MYF+GDGARRD DGYYWITGRVDDVLNVSGHR+GTAEIESALV+HP
Sbjct: 481 HDRFEQTYFSTFKGMYFTGDGARRDSDGYYWITGRVDDVLNVSGHRMGTAEIESALVSHP 540

Query: 541 KIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAAVVG+PH IKGQ IYAYVTLN GE PSPELYAEV+ WVRKEIG +ATPD+LHW +
Sbjct: 541 KIAEAAVVGVPHEIKGQGIYAYVTLNEGEYPSPELYAEVKQWVRKEIGAIATPDILHWAE 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
            LPKTRSGKIMRRILRKIA G++ +LGD STLADP VVE+L++E +
Sbjct: 601 GLPKTRSGKIMRRILRKIATGESDSLGDISTLADPSVVEQLIKENR 646


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: 1567
Number of extensions: 61
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_011771371.1 PING_RS16055 (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.3044081.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 1019.0   0.1          0 1018.8   0.1    1.0  1  NCBI__GCF_000015285.1:WP_011771371.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015285.1:WP_011771371.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.8   0.1         0         0       4     628 ..      21     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1018.8 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           +eey + y+ +i+dp++fw++++k  l+w+kp++kv+++s+++   ++kWfedg+lnvs+nc+drh++++ d+
  NCBI__GCF_000015285.1:WP_011771371.1  21 NEEYLTQYQASISDPSAFWGEKGK-ILDWIKPYTKVKNSSFDSghvSIKWFEDGKLNVSANCIDRHLATKGDQ 92 
                                           789********************9.6**************9988889************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vai wegd +++  +k+tY++l+++vc++anvlk++Gv+kgd v++Y+pm+pea++amlac+RiGavhs+vf+
  NCBI__GCF_000015285.1:WP_011771371.1  93 VAILWEGDTADK-DEKITYKQLHQRVCQFANVLKSQGVRKGDVVCLYMPMTPEAAVAMLACTRIGAVHSIVFG 164
                                           ********7775.99********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs++a+a Rivd++ak+vitadeg Rgg+v++lk++vdeal+k  +  v++v+v+k tg ev+ w+ grD+ 
  NCBI__GCF_000015285.1:WP_011771371.1 165 GFSPDAIAGRIVDSSAKIVITADEGRRGGRVVPLKANVDEALTKDGTdCVKSVIVFKNTGGEVN-WVVGRDLD 236
                                           *******************************************998889*************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           we+++++ +s+ecepe++++edplfiLYtsGstG+PkGvlhttgGyl++aa+t+kyvfd++++di+wCtaDvG
  NCBI__GCF_000015285.1:WP_011771371.1 237 WESVCAD-ESSECEPEAMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYAAMTFKYVFDYQEGDIYWCTADVG 308
                                           ******7.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           W+tGh+Y vygPLanGat+l+fegvp+yp+++r+ ev++k+kv+i+YtaPtaiRalm++g+++++ +++sslr
  NCBI__GCF_000015285.1:WP_011771371.1 309 WITGHTYSVYGPLANGATSLIFEGVPNYPTPARMSEVVDKHKVSILYTAPTAIRALMAKGDQAIEGTHRSSLR 381
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lgsvGepinpeaweWyy+++G+e+cpivdtwWqtetGgili+plpg at+lkpgsat+P+fG+++++vd+eg
  NCBI__GCF_000015285.1:WP_011771371.1 382 ILGSVGEPINPEAWEWYYNKIGDERCPIVDTWWQTETGGILISPLPG-ATDLKPGSATRPFFGVQPAIVDSEG 453
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                             +e e+  g Lv+ ++wP+++rt+y++++rf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsGh
  NCBI__GCF_000015285.1:WP_011771371.1 454 VVLEGEAA-GNLVMLDSWPGQMRTLYNNHDRFEQTYFSTFKGMYFTGDGARRDSDGYYWITGRVDDVLNVSGH 525
                                           ***98777.89************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtaeiesalvsh+++aeaavvgvp+eikg+ i+a+v+l+eg+ ++ e l +e+k++vrkeig+ia+pd ++
  NCBI__GCF_000015285.1:WP_011771371.1 526 RMGTAEIESALVSHPKIAEAAVVGVPHEIKGQGIYAYVTLNEGEYPSPE-LYAEVKQWVRKEIGAIATPDILH 597
                                           ************************************************5.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++e lPktRsGkimRR+lrkia+ge ++lgd+stl+dpsvve+l++
  NCBI__GCF_000015285.1:WP_011771371.1 598 WAEGLPKTRSGKIMRRILRKIATGEsDSLGDISTLADPSVVEQLIK 643
                                           *************************99****************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: 00:00:00.02
# Mc/sec: 19.47
//
[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:

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:

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:

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:

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