GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinobacter algicola DG893

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_007152037.1 MDG893_RS01990 acetate--CoA ligase

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



>NCBI__GCF_000170835.1:WP_007152037.1
          Length = 648

 Score =  963 bits (2489), Expect = 0.0
 Identities = 459/642 (71%), Positives = 530/642 (82%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           M+   +YPV P+VA   L +   Y+ MYQQSV +P+ FW E  KRLDWIKPF+ VK T++
Sbjct: 1   MTDKQVYPVSPDVAKRALLNRDQYEKMYQQSVEDPETFWAEHGKRLDWIKPFSKVKNTTY 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           D  ++ IKWF DG LN + NCLDRHL +RGDQ AII+EGDDP++SRN+TYREL+EE CKF
Sbjct: 61  DYDNLSIKWFEDGQLNAAANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELYEETCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           AN L+ Q V +GDVVTIYMPMI E  VAMLAC RIGAIHSVVFGGFSPEAL  RI + KS
Sbjct: 121 ANVLKDQGVKKGDVVTIYMPMIVETGVAMLACARIGAIHSVVFGGFSPEALGARIANGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           + V+TADEGVR G+KIPLK NVD AL+  + + + KVIV KRT G++ W   RD  YE+L
Sbjct: 181 RFVVTADEGVRGGRKIPLKKNVDAALSKEDGADVDKVIVVKRTGGDVPWKDGRDQSYEEL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           MKVA + C  + M AE+ LF+LYTSGSTG PKGV HTT GY++Y ++THE VFDY+ G+V
Sbjct: 241 MKVASSDCPAEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYTSMTHEYVFDYQDGDV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTAD GWVTGHSYI+YGPLANGA T+LFEGVPNYPD +R+ +V+DKHKV+ILYTAPTA
Sbjct: 301 YWCTADFGWVTGHSYILYGPLANGAVTVLFEGVPNYPDTSRMGQVVDKHKVNILYTAPTA 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G + + G    SLRLLGSVGEPINPEAW+WY++ +G  +CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGESCMNGTTRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGA  LKPGSAT PFFGV PALVDN GN++EG  EGNLVILDSWPGQ RT+YGD
Sbjct: 421 ILISPLPGAIDLKPGSATVPFFGVKPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RF  TYF T+ GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+VAH 
Sbjct: 481 HERFKQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVAHD 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVG PH+IKGQGIYVYVTL  GEE S+ L+ EL  WVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGYPHEIKGQGIYVYVTLVHGEEPSDELKKELVQWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           GLPKTRSGKIMRRILRKIA+ E+D LGD STLADPGVV  LI
Sbjct: 601 GLPKTRSGKIMRRILRKIASNEHDQLGDTSTLADPGVVDDLI 642


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: 1480
Number of extensions: 57
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: 648
Length adjustment: 38
Effective length of query: 613
Effective length of database: 610
Effective search space:   373930
Effective search space used:   373930
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_007152037.1 MDG893_RS01990 (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.1609341.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 1027.6   0.0          0 1027.4   0.0    1.0  1  NCBI__GCF_000170835.1:WP_007152037.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170835.1:WP_007152037.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1027.4   0.0         0         0       3     627 ..      20     642 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1027.4 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           + ++y+++y++++edpe+fwa+++k +l+w+kpf+kv++++ +    ++kWfedg+ln+++nc+drh+ekr d
  NCBI__GCF_000170835.1:WP_007152037.1  20 NRDQYEKMYQQSVEDPETFWAEHGK-RLDWIKPFSKVKNTTYDYdnlSIKWFEDGQLNAAANCLDRHLEKRGD 91 
                                           679**********************.5***********9987665589************************* PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           ++aii+egd++  dsr++tY+el++e+c++anvlk++Gvkkgd v+iY+pmi+e+ +amlacaRiGa+hsvvf
  NCBI__GCF_000170835.1:WP_007152037.1  92 QTAIIFEGDDPA-DSRNVTYRELYEETCKFANVLKDQGVKKGDVVTIYMPMIVETGVAMLACARIGAIHSVVF 163
                                           ***********9.5*********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDv 217
                                           +Gfs+eal  Ri + ++++v+tadeg+Rgg++i+lkk+vd+al+k++  +v+kv+vvkrtg +v  wk+grD 
  NCBI__GCF_000170835.1:WP_007152037.1 164 GGFSPEALGARIANGKSRFVVTADEGVRGGRKIPLKKNVDAALSKEDGaDVDKVIVVKRTGGDVP-WKDGRDQ 235
                                           ********************************************99988**************66.******* PP

                             TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290
                                            +eel++  as++c++e++++edplf+LYtsGstG PkGvlhttgGy++++++t++yvfd++d+d++wCtaD 
  NCBI__GCF_000170835.1:WP_007152037.1 236 SYEELMKV-ASSDCPAEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYTSMTHEYVFDYQDGDVYWCTADF 307
                                           *******5.**************************************************************** PP

                             TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363
                                           GWvtGhsYi+ygPLanGa t+lfegvp+ypd+sr+ +v++k+kv+i+YtaPtaiRalm++ge+ ++ + ++sl
  NCBI__GCF_000170835.1:WP_007152037.1 308 GWVTGHSYILYGPLANGAVTVLFEGVPNYPDTSRMGQVVDKHKVNILYTAPTAIRALMAEGESCMNGTTRDSL 380
                                           ************************************************************************* PP

                             TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436
                                           r+lgsvGepinpeaweWy++v+G++kcpivdtwWqtetGgili+plpg a++lkpgsat+P+fG+++++vd++
  NCBI__GCF_000170835.1:WP_007152037.1 381 RLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGILISPLPG-AIDLKPGSATVPFFGVKPALVDND 452
                                           ************************************************.6*********************** PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           g+ +e ++e g Lvi ++wP+++rtiygd+erf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsG
  NCBI__GCF_000170835.1:WP_007152037.1 453 GNILEGKTE-GNLVILDSWPGQMRTIYGDHERFKQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSG 524
                                           *****8777.79************************************************************* PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           hrlgtae+esalv+h++vaeaavvg+p+eikg+ i+++v+l +g+e+++e l+kel ++vrkeigpia+pd i
  NCBI__GCF_000170835.1:WP_007152037.1 525 HRLGTAEVESALVAHDKVAEAAVVGYPHEIKGQGIYVYVTLVHGEEPSDE-LKKELVQWVRKEIGPIASPDVI 596
                                           *************************************************5.********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           ++++ lPktRsGkimRR+lrkia++e ++lgd+stl+dp vv++l+
  NCBI__GCF_000170835.1:WP_007152037.1 597 QWAPGLPKTRSGKIMRRILRKIASNEhDQLGDTSTLADPGVVDDLI 642
                                           **************************9****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (648 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.23
//
[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