GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Methanospirillum stamsii Pt1

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_109940435.1 DLD82_RS07210 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_003173335.1:WP_109940435.1
          Length = 630

 Score =  690 bits (1780), Expect = 0.0
 Identities = 327/629 (51%), Positives = 452/629 (71%), Gaps = 5/629 (0%)

Query: 7   VLLEEKRVFKPHYTVVEEAHIKNW-EAELEKGKDHENYWAEKAERLEWFRKWDRVLDESN 65
           VL  +++V+ P  +    A I+++ E   E  KD + +W   A  L WF++WD V    +
Sbjct: 6   VLKPDQKVYYPDPSYQNSALIRDYDELYREFEKDPDAFWRRIASDLLWFKQWDTVRTWDH 65

Query: 66  RPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANA 125
            P   WF N ++N+TYN ++R ++ D+RN+VAI +  E G ER LTYY+LY++V R  NA
Sbjct: 66  -PHASWFTNAELNITYNCLERHVNNDRRNKVAIFWAGENGKERILTYYQLYKDVMRMGNA 124

Query: 126 LKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKII 185
           LKSLG++KGD V +YLP  PELVVSMLACA+IGAVH+V+++G    AL ER+  A AKI+
Sbjct: 125 LKSLGVRKGDRVCIYLPGIPELVVSMLACARIGAVHTVVFAGYGAKALNERITGAGAKIV 184

Query: 186 ITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEG 245
           ITAD + RRGG I LKPIV+EA++  PT+E  ++++  +  + + D    E+ +++LI  
Sbjct: 185 ITADASVRRGGSIPLKPIVEEALIHAPTVEKVIILRTQEPKVGLLD--DFELDYEELISQ 242

Query: 246 EGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWC 305
               C+ E +++EDPLFILYTSG+TG PKG++HT GGYMVG   T +    +   D++WC
Sbjct: 243 ADRNCEPEHVNSEDPLFILYTSGTTGAPKGIVHTAGGYMVGAYYTTKYVLTLRENDVYWC 302

Query: 306 TADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRH 365
           TAD GWITGH+Y +YGPLL+G T  L E  PDYPD G+WW ++E+YGVT FYTAPTAIR 
Sbjct: 303 TADPGWITGHTYGIYGPLLVGGTIFLTEYTPDYPDAGIWWKLIEEYGVTIFYTAPTAIRM 362

Query: 366 LMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLI 425
            MR G++  ++Y+L SL++LG+VGEP+NPEA+ W+Y++IG++ CPI+DTWWQTETGMH+I
Sbjct: 363 FMRMGEEWSEKYDLSSLRLLGSVGEPLNPEAFEWFYKHIGKKNCPILDTWWQTETGMHMI 422

Query: 426 APLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQRY 485
             +   P+KPG   KP+PG+ A VV+E GDPVP G  GFL I++PWP+M +T++ +++RY
Sbjct: 423 TTMVGLPMKPGFAGKPIPGVVATVVNEEGDPVPPGTNGFLAIKEPWPSMMKTVYQNDERY 482

Query: 486 IDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVA 545
              YW     G Y++ D+A  DEDGY  + GRSDD++ +AGH +GTAE+ES  V+H AVA
Sbjct: 483 RQ-YWNFGKYGYYSSNDIAMMDEDGYIMLLGRSDDIIIVAGHNVGTAEIESALVSHSAVA 541

Query: 546 EAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLP 605
           EAA IGK DP+KG +IKAF+IL+ G      LI +LK H+R  LGP++V  E+  VD+LP
Sbjct: 542 EAAAIGKPDPLKGNIIKAFVILRNGVSPTPKLIHDLKYHVRIMLGPISVPAELDFVDNLP 601

Query: 606 KTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           KTRSGKIMRR+L+A+E G D GD STL+E
Sbjct: 602 KTRSGKIMRRVLKAQEMGIDPGDVSTLDE 630


Lambda     K      H
   0.319    0.138    0.428 

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: 1286
Number of extensions: 62
Number of successful extensions: 4
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: 634
Length of database: 630
Length adjustment: 38
Effective length of query: 596
Effective length of database: 592
Effective search space:   352832
Effective search space used:   352832
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_109940435.1 DLD82_RS07210 (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.2499816.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-252  825.7   0.0   1.3e-252  825.5   0.0    1.0  1  NCBI__GCF_003173335.1:WP_109940435.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003173335.1:WP_109940435.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.5   0.0  1.3e-252  1.3e-252       4     618 ..      26     629 ..      23     630 .] 0.97

  Alignments for each domain:
  == domain 1  score: 825.5 bits;  conditional E-value: 1.3e-252
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           +++y ely+e ++dp++fw++ a++ l w+k++++v++++ +p++ Wf+++eln++ync++rhv++ r++kva
  NCBI__GCF_003173335.1:WP_109940435.1  26 IRDYDELYREFEKDPDAFWRRIASD-LLWFKQWDTVRTWD-HPHASWFTNAELNITYNCLERHVNNdRRNKVA 96 
                                           578*********************6.*************9.779*********************99****** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           i w g++ +  +r ltY++l+++v r+ n+lk+lGv+kgdrv+iYlp ipe+v+ mlacaRiGavh+vvfaG+
  NCBI__GCF_003173335.1:WP_109940435.1  97 IFWAGENGK--ERILTYYQLYKDVMRMGNALKSLGVRKGDRVCIYLPGIPELVVSMLACARIGAVHTVVFAGY 167
                                           ******665..6************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                            a+al+eRi+ a ak+vitad ++R+g +i+lk iv+eal +a+ +vekv++++ ++ +v  + ++ ++ +ee
  NCBI__GCF_003173335.1:WP_109940435.1 168 GAKALNERITGAGAKIVITADASVRRGGSIPLKPIVEEALIHAP-TVEKVIILRTQEPKVG-LLDDFELDYEE 238
                                           *******************************************9.7*******99998866.999******** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           l+++ a+++cepe+++sedplfiLYtsG+tG PkG++ht+gGy++ a++t+kyv  ++++d++wCtaD GW+t
  NCBI__GCF_003173335.1:WP_109940435.1 239 LISQ-ADRNCEPEHVNSEDPLFILYTSGTTGAPKGIVHTAGGYMVGAYYTTKYVLTLRENDVYWCTADPGWIT 310
                                           ***6.******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           Gh+Y +ygPL++G t +l e +p+ypda+ +w++ie+y+vtifYtaPtaiR++m++gee+ +k+dlsslr+lg
  NCBI__GCF_003173335.1:WP_109940435.1 311 GHTYGIYGPLLVGGTIFLTEYTPDYPDAGIWWKLIEEYGVTIFYTAPTAIRMFMRMGEEWSEKYDLSSLRLLG 383
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGep+npea+eW+y+++Gk++cpi dtwWqtetG ++it++ g  +++kpg a +P++G+ a+vv+eeg++v
  NCBI__GCF_003173335.1:WP_109940435.1 384 SVGEPLNPEAFEWFYKHIGKKNCPILDTWWQTETGMHMITTMVG--LPMKPGFAGKPIPGVVATVVNEEGDPV 454
                                           ********************************************..5************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                            ++++ g+L+ik+pwPsm++t+y+++er+ + Y++  k  +y + D a++d+dGyi++lGR Dd+i v+Gh++
  NCBI__GCF_003173335.1:WP_109940435.1 455 PPGTN-GFLAIKEPWPSMMKTVYQNDERYRQ-YWNFGKYgYYSSNDIAMMDEDGYIMLLGRSDDIIIVAGHNV 525
                                           **999.8**********************86.6664444389999**************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtaeiesalvsh+avaeaa++g+pd +kg++i afv+l++gv+++  +l ++lk +vr ++gpi+ p+++ +v
  NCBI__GCF_003173335.1:WP_109940435.1 526 GTAEIESALVSHSAVAEAAAIGKPDPLKGNIIKAFVILRNGVSPTP-KLIHDLKYHVRIMLGPISVPAELDFV 597
                                           **********************************************.5************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaegeellgdvstle 618
                                           ++lPktRsGkimRR+l++   g +  gdvstl+
  NCBI__GCF_003173335.1:WP_109940435.1 598 DNLPKTRSGKIMRRVLKAQEMGID-PGDVSTLD 629
                                           ****************98766655.56****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (630 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: 32.02
//
[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