GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella loihica PV-4

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 5209055 Shew_1533 acetyl-CoA synthetase (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__PV4:5209055
          Length = 650

 Score =  984 bits (2544), Expect = 0.0
 Identities = 461/644 (71%), Positives = 537/644 (83%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  SLY V  E+AA+   ++  YK MYQ+SVVNP+GFWRE  +R+DW+KPFT VK+TSF
Sbjct: 1   MSTQSLYKVPSEIAANAHINDEKYKKMYQESVVNPEGFWREHGQRIDWMKPFTKVKKTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDH++ I WF DGTLN S NCLDRHLA+  D++AIIWEGDD ++ R +TY ELH EVCKF
Sbjct: 61  DDHNLSINWFYDGTLNASVNCLDRHLADNADKLAIIWEGDDAADQRTLTYGELHTEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALR Q V RGDVVT+YMPM+PEA V MLAC RIGAIHSVVFGGFSP+++A R+ID KS
Sbjct: 121 ANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR G+ IPLKAN+D+AL++P+ + ++KVIV +RT   + W + RDI +  L
Sbjct: 181 KVVITADEGVRGGRTIPLKANIDEALSHPDVTCVEKVIVLERTGNPVNWVEGRDIKWASL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           M+ A   C  +EMGAE+ LF+LYTSGSTG PKGV HTT GYL+YA++THE VFDYK GE+
Sbjct: 241 METASEHCVAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEI 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PNYP   R+ ++ID+HKV+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNYPTPARLGEMIDRHKVNILYTAPTL 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G    +G DGSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHENCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT  KPGSATRPFFGV PALVDN+GN+I+GAAEGNLVILDSWPGQ RT+YGD
Sbjct: 421 ILISPLPGATDTKPGSATRPFFGVQPALVDNMGNIIDGAAEGNLVILDSWPGQMRTVYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRF  TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH 
Sbjct: 481 HDRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHE 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
            VAEAAVVG PHDIKGQGIY YVTL  G + SE LR EL+ WVRKEIG +A+PD+IQWA 
Sbjct: 541 HVAEAAVVGYPHDIKGQGIYAYVTLTKGTQESEELRQELRQWVRKEIGALATPDLIQWAG 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIET
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIDTLIET 644


Lambda     K      H
   0.318    0.135    0.418 

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: 1474
Number of extensions: 50
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: 651
Length of database: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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 5209055 Shew_1533 (acetyl-CoA synthetase (RefSeq))
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.17572.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 1021.6   0.1          0 1021.4   0.1    1.0  1  lcl|FitnessBrowser__PV4:5209055  Shew_1533 acetyl-CoA synthetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209055  Shew_1533 acetyl-CoA synthetase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.4   0.1         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1021.4 bits;  conditional E-value: 0
                        TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 
                                      + e+yk++y+e++ +pe fw+++++ +++w+kpf+kv+++s+++   +++Wf dg+ln+s+nc+drh+++++dk+aii
  lcl|FitnessBrowser__PV4:5209055  20 NDEKYKKMYQESVVNPEGFWREHGQ-RIDWMKPFTKVKKTSFDDhnlSINWFYDGTLNASVNCLDRHLADNADKLAII 96 
                                      5689********************9.5*************99887789****************************** PP

                        TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealae 155
                                      wegd++  d+r+ltY el++evc++an+l+++Gv++gd v++Y+pm+pea+++mlacaRiGa+hsvvf+Gfs++++a+
  lcl|FitnessBrowser__PV4:5209055  97 WEGDDAA-DQRTLTYGELHTEVCKFANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIAS 173
                                      ****998.6********************************************************************* PP

                        TIGR02188 156 RivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaece 232
                                      R++d ++k+vitadeg+Rgg++i+lk+++deal++ +   vekv+v++rtg++v+ w+egrD++w +l+e+ as++c 
  lcl|FitnessBrowser__PV4:5209055 174 RVIDGKSKVVITADEGVRGGRTIPLKANIDEALSHPDVtCVEKVIVLERTGNPVN-WVEGRDIKWASLMET-ASEHCV 249
                                      ***********************************99989*************66.**************6.****** PP

                        TIGR02188 233 pekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGatt 310
                                      +e++++edplf+LYtsGstG+PkGvlhttgGyl++a++t++yvfd+k+++i+wCtaDvGW+tGhsY+vygPLanGat 
  lcl|FitnessBrowser__PV4:5209055 250 AEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEIYWCTADVGWITGHSYMVYGPLANGATI 327
                                      ****************************************************************************** PP

                        TIGR02188 311 llfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGke 388
                                      l++eg+p+yp+++r+ e+i+++kv+i+YtaPt+iRalm++g+e+++  d sslr++gsvGepinpeaw+Wy+ev+G+e
  lcl|FitnessBrowser__PV4:5209055 328 LIHEGIPNYPTPARLGEMIDRHKVNILYTAPTLIRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHE 405
                                      ****************************************************************************** PP

                        TIGR02188 389 kcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygde 466
                                      +cpivdtwWqtetGgili+plpg at++kpgsat+P+fG+++++vd+ g+ ++  +e g Lvi ++wP+++rt+ygd+
  lcl|FitnessBrowser__PV4:5209055 406 NCPIVDTWWQTETGGILISPLPG-ATDTKPGSATRPFFGVQPALVDNMGNIIDGAAE-GNLVILDSWPGQMRTVYGDH 481
                                      ***********************.6****************************8777.79****************** PP

                        TIGR02188 467 erfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeai 544
                                      +rf  tYfk+++g+yftGDgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalv+he+vaeaavvg+p++ikg+ i
  lcl|FitnessBrowser__PV4:5209055 482 DRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHEHVAEAAVVGYPHDIKGQGI 559
                                      ****************************************************************************** PP

                        TIGR02188 545 vafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621
                                      +a+v+l++g++e+e el++el+++vrkeig++a+pd i+++  lPktRsGkimRR+lrkia++e ++lgd stl+dp+
  lcl|FitnessBrowser__PV4:5209055 560 YAYVTLTKGTQESE-ELRQELRQWVRKEIGALATPDLIQWAGGLPKTRSGKIMRRFLRKIAANEvTNLGDASTLADPA 636
                                      ***********999.5************************************************************** PP

                        TIGR02188 622 vveelke 628
                                      v+++l+e
  lcl|FitnessBrowser__PV4:5209055 637 VIDTLIE 643
                                      ***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (650 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.14
//
[ok]

This GapMind analysis is from Sep 17 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