GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Desulfurobacterium atlanticum DSM 15668

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_089322819.1 CHB58_RS03975 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_900188395.1:WP_089322819.1
          Length = 631

 Score =  732 bits (1889), Expect = 0.0
 Identities = 356/628 (56%), Positives = 467/628 (74%), Gaps = 6/628 (0%)

Query: 8   LLEEKRVFKPHYTVVEEAHIKNWEAELEKGKDH-ENYWAEKAERLEWFRKWDRVLDESNR 66
           LL    + KP    V  A++KN+E E +K  D+ E +WA+ A+ L W+ KWD+VL E N 
Sbjct: 9   LLHLGTIIKPPEEFVRNANVKNYEEEYKKFLDNPEEFWAKVADELFWYEKWDKVL-EWNL 67

Query: 67  PFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANAL 126
           P+ +WFVNGK N+T NA+DR +   ++N+VA  + +E G+E+ +TY  LY  V++ ANAL
Sbjct: 68  PYAKWFVNGKTNITVNALDRHVKNGRKNKVAFFWEDEFGNEKVVTYGSLYTLVNKLANAL 127

Query: 127 KSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKIII 186
           K+ GIKKGD V +Y+P+  E V +MLACA+IGAVHSV+Y+G SV AL  R+ DA+AK++I
Sbjct: 128 KNAGIKKGDRVVIYMPLVVEQVAAMLACARIGAVHSVVYAGFSVPALRHRIEDAQAKMVI 187

Query: 187 TADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEGE 246
           TAD T RRG  I LK IVDEA+     +E  VV++     +++  I  +E+ F + I+  
Sbjct: 188 TADMTIRRGRAIPLKQIVDEAVRGLDNVEKVVVLRRLKPKVDL--IGEKEIDFYEFIKDA 245

Query: 247 GDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWCT 306
              C+ E MD+EDPLF+LYTSGSTGKPKGV+HTTGGYMVG   +++  FD+   D++WCT
Sbjct: 246 DTYCEPEVMDSEDPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLKEDDIYWCT 305

Query: 307 ADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRHL 366
           AD GWITGHSY+VYGPL+ G T +L EGAP+YPD G WWS++EKYGVT FYTAPTAIR  
Sbjct: 306 ADPGWITGHSYIVYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYTAPTAIRMF 365

Query: 367 MRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLIA 426
           MR G+  P++Y+L SL++LG+VGEPINPEAWMWY+R IG+E+CPI+DTWWQTETG  +I 
Sbjct: 366 MRAGEHWPEKYDLSSLRLLGSVGEPINPEAWMWYFRVIGKERCPIVDTWWQTETGAVMIT 425

Query: 427 PLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQRYI 486
            +   P+KPG   KP+PG+ ADVVD+ G+PV   KGGFLV+R PWP+M RT+  ++++Y 
Sbjct: 426 TIDGLPMKPGRAGKPVPGVVADVVDKEGNPVEPNKGGFLVVRNPWPSMMRTIHKNKEKY- 484

Query: 487 DVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVAE 546
           + YW  IP G Y AGD+A KDEDGY  I GR+DDV+N++GHRIGT EVES  V+HP+VAE
Sbjct: 485 ESYWNTIP-GCYFAGDVATKDEDGYIMILGRADDVINVSGHRIGTMEVESALVSHPSVAE 543

Query: 547 AAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLPK 606
           AAVIGK DP+KGE IKAF+ILK+G   +  L+  LK+H+R ELG +AV  E+  VD LPK
Sbjct: 544 AAVIGKPDPVKGERIKAFVILKEGESPSEELVNSLKKHVRTELGALAVPSEIEFVDKLPK 603

Query: 607 TRSGKIMRRILRAREEGEDLGDTSTLEE 634
           TRSGKIMRR+L+A+E G D GD STLE+
Sbjct: 604 TRSGKIMRRVLKAKELGMDPGDLSTLED 631


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: 1241
Number of extensions: 59
Number of successful extensions: 6
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: 631
Length adjustment: 38
Effective length of query: 596
Effective length of database: 593
Effective search space:   353428
Effective search space used:   353428
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_089322819.1 CHB58_RS03975 (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.3109051.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-279  914.4   0.3   1.8e-279  914.2   0.3    1.0  1  NCBI__GCF_900188395.1:WP_089322819.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188395.1:WP_089322819.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  914.2   0.3  1.8e-279  1.8e-279       3     619 ..      27     631 .]      25     631 .] 0.98

  Alignments for each domain:
  == domain 1  score: 914.2 bits;  conditional E-value: 1.8e-279
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                           ++++y+e y++  ++pe+fwak a  el w ++++kvl+++  p +kWf++g++n+++n++drhv++ rk+kv
  NCBI__GCF_900188395.1:WP_089322819.1  27 NVKNYEEEYKKFLDNPEEFWAKVAD-ELFWYEKWDKVLEWN-LPYAKWFVNGKTNITVNALDRHVKNgRKNKV 97 
                                           7899********************9.5*************9.569**************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a  we +  g+ ++ +tY  l++ v++lan+lk++G+kkgdrv+iY+p+++e v+amlacaRiGavhsvv+aG
  NCBI__GCF_900188395.1:WP_089322819.1  98 AFFWEDE-FGN-EKVVTYGSLYTLVNKLANALKNAGIKKGDRVVIYMPLVVEQVAAMLACARIGAVHSVVYAG 168
                                           *****98.554.7************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs  al++Ri+da+ak+vitad ++R+g++i+lk+ivdea++  + +vekv+v++r + +v  +  ++++ + 
  NCBI__GCF_900188395.1:WP_089322819.1 169 FSVPALRHRIEDAQAKMVITADMTIRRGRAIPLKQIVDEAVRGLD-NVEKVVVLRRLKPKVD-LIGEKEIDFY 239
                                           *******************************************98.7*************76.9999****** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e +++ a+++cepe +dsedplf+LYtsGstGkPkGv+httgGy++ +++++k+vfd+k++di+wCtaD GW+
  NCBI__GCF_900188395.1:WP_089322819.1 240 EFIKD-ADTYCEPEVMDSEDPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLKEDDIYWCTADPGWI 311
                                           ****7.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivygPL++Gat++l eg+p+ypd +r+w++ieky+vtifYtaPtaiR++m++ge++++k+dlsslr+l
  NCBI__GCF_900188395.1:WP_089322819.1 312 TGHSYIVYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYTAPTAIRMFMRAGEHWPEKYDLSSLRLL 384
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw+Wy++v+Gke+cpivdtwWqtetG+++it++ g  +++kpg a +P++G+ a+vvd+eg++
  NCBI__GCF_900188395.1:WP_089322819.1 385 GSVGEPINPEAWMWYFRVIGKERCPIVDTWWQTETGAVMITTIDG--LPMKPGRAGKPVPGVVADVVDKEGNP 455
                                           *********************************************..5************************* PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ve++++ g+Lv+++pwPsm+rti++++e++ e+Y+++++g+yf+GD a++d+dGyi+ilGR+DdvinvsGhr+
  NCBI__GCF_900188395.1:WP_089322819.1 456 VEPNKG-GFLVVRNPWPSMMRTIHKNKEKY-ESYWNTIPGCYFAGDVATKDEDGYIMILGRADDVINVSGHRI 526
                                           ***999.8********************98.68**************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gt+e+esalvsh++vaeaav+g+pd +kge i afv+lkeg++++ee l ++lkk+vr+e+g++a p++i++v
  NCBI__GCF_900188395.1:WP_089322819.1 527 GTMEVESALVSHPSVAEAAVIGKPDPVKGERIKAFVILKEGESPSEE-LVNSLKKHVRTELGALAVPSEIEFV 598
                                           *********************************************95.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaegeellgdvstled 619
                                           ++lPktRsGkimRR+l++   g    gd+stled
  NCBI__GCF_900188395.1:WP_089322819.1 599 DKLPKTRSGKIMRRVLKAKELG-MDPGDLSTLED 631
                                           ****************986655.5567*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (631 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: 30.63
//
[ok]

This GapMind analysis is from Apr 09 2024. 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