GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Bacillus altitudinis 41KF2b

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_035704411.1 BA79_RS18200 AMP-binding protein

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000691145.1:WP_035704411.1
          Length = 644

 Score =  385 bits (988), Expect = e-111
 Identities = 220/595 (36%), Positives = 338/595 (56%), Gaps = 18/595 (3%)

Query: 43  YW--AEKAERLEWFRKWDRVLDESNRPFYRWFVNGKINMTYNAVDRWLDTDK-RNQVAIL 99
           +W  AEKA  ++W + ++  L   +  + +W+  G +N+T  AVD+W + ++ ++Q AI+
Sbjct: 46  FWREAEKAVGIQWKKPYEAALGHHSLMWPKWYQGGTLNITETAVDKWAEKEETKHQPAII 105

Query: 100 YVNERGDERKLTYYELYREVSRTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGA 159
           + NE G+E+K ++ EL  +VSR A      G++KGD   +Y+PM PE V  MLA  KIG 
Sbjct: 106 WSNEAGEEKKWSFLELQEKVSRLAAGFLKEGLQKGDVAIIYMPMLPETVAVMLAFTKIGV 165

Query: 160 VHSVIYSGLSVGALVERLNDARAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVV 219
           + S ++SG     L  R+  + A I++TA+   RRG  I ++  V +AI +  T++  +V
Sbjct: 166 IFSPVFSGYGSEPLAVRIRASGASIVVTANEMMRRGKTINMRECVADAINKTATVQKVIV 225

Query: 220 VKHTDIDIEMSDISGREMLFDKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHT 279
              +    +  D+   ++L ++ I G      A  +  EDPL ILYTSG+TG PKG +HT
Sbjct: 226 HTSSHTGYQ-GDVLLNDLLQEQPITG------ATYVTNEDPLMILYTSGTTGTPKGAVHT 278

Query: 280 TGGYMVGVASTLEMTFDIHNGD-LWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDY 338
             G+ +  A    +  D+  GD L+W T D+GW+ G  ++V+G L+ G   +LY+GAPDY
Sbjct: 279 HAGFPIKAAFDAGLCMDVAKGDRLFWLT-DMGWMMG-PFLVFGGLINGAAIVLYDGAPDY 336

Query: 339 PDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWM 398
           PD    WS + +  VT F  +PT +R  M+   +      L  +K + + GEP N   W 
Sbjct: 337 PDEQQLWSFIHQKKVTHFGLSPTFVRSAMQ---QTIDGVELSHVKAIISTGEPWNEAPWQ 393

Query: 399 WYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVP 458
           W +  IG++  PI++    TE    ++    + P+KP      + G+ ADV +E G  V 
Sbjct: 394 WLFHTIGQKNIPILNYSGGTEVSGGIVGSTLLRPIKPILFNAAILGMAADVYNEAGQSV- 452

Query: 459 LGKGGFLVIRKPWPAMFRTLFNDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRS 518
           + + G LV++KPW  M    +N+ +RY D Y+K+  G V+T GD   + EDG F I GRS
Sbjct: 453 MNEVGELVVKKPWVGMTCGFWNEPERYEDTYFKRFDG-VWTHGDWVMQTEDGEFHITGRS 511

Query: 519 DDVLNIAGHRIGTAEVESVFVAHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALI 578
           DDV+N AG RIG AE+ES+   HPAV EAAVIG  D +KGE +  F++        A LI
Sbjct: 512 DDVINTAGKRIGPAEIESILTWHPAVHEAAVIGVKDEVKGEALVCFIVTSPHAFEEATLI 571

Query: 579 EELKRHLRHELGPVAVVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLE 633
           +EL  H+    G      E+  + +LPKTR+GKI+RR+L+   E +   D S+L+
Sbjct: 572 QELSAHVGSHAGKALTPKEVHLISALPKTRNGKIVRRLLKGAYEEKPSPDLSSLD 626


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: 1119
Number of extensions: 65
Number of successful extensions: 7
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: 644
Length adjustment: 38
Effective length of query: 596
Effective length of database: 606
Effective search space:   361176
Effective search space used:   361176
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)

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