GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Bacillus altitudinis 41KF2b

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_035704422.1 BA79_RS18230 AMP-binding protein

Query= metacyc::MONOMER-20125
         (556 letters)



>NCBI__GCF_000691145.1:WP_035704422.1
          Length = 545

 Score =  214 bits (544), Expect = 9e-60
 Identities = 162/541 (29%), Positives = 259/541 (47%), Gaps = 57/541 (10%)

Query: 32  SVVYD--AVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGA 89
           +VVY   ++ Y++   ++        + +LG++ G  ++++APN+P+   L FA    GA
Sbjct: 25  AVVYPERSLRYSYEAFYQEVKATGKGLMALGVQKGDHIAIMAPNIPEWLILQFACASIGA 84

Query: 90  ILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESE 149
           +L  VN    ++ ++ LL HS+SK++F+           +  F + + V  L  +  E +
Sbjct: 85  VLVTVNTNFQSQELAYLLKHSDSKMLFI-----------VDGFKETSYVNMLEELIPELQ 133

Query: 150 SGNSSELGKEFFCSYKDLIDRGD-------------------PDFKWVMPKSEWDP---M 187
           + +  E+    F   K  I  G                     D +W    +E  P   +
Sbjct: 134 TAHQEEITSTQFPYLKRCIYIGQHVPNGMLSWDRLQVAAKRTEDHEWEKRMNELTPDDVI 193

Query: 188 ILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMA 247
            + YTSGTT  PKGV+  H  I            + +Q      +P FH  G S    +A
Sbjct: 194 NMQYTSGTTGYPKGVMLSHTNIVCNASQIADCMKLTEQDRMCIPVPFFHCFG-SVLGVLA 252

Query: 248 AV--GGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPG--SEPLKTTVQIMT 303
            +  GGT I L  F  E +   +++   T + G P +     + P   S  L T    + 
Sbjct: 253 CLTKGGTIIPLESFHPERVLQTVEKEKCTVLHGVPTMFIAELDHPNFHSYDLSTLRTGIM 312

Query: 304 AGAPPPSAVLFRT-ESLGFA-VSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQG 361
           AG+  PS V+    E +G   ++  YG TE++ ++              T+ +  +  Q 
Sbjct: 313 AGSLCPSHVMKAVIEKMGLRELTIAYGQTESSPVITQTR----------TDDSFERRVQT 362

Query: 362 VGTVM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFY 420
           VG  + Q ++ +  P T   V R     GE+  RG  VM GY K+ E T + +  DGW +
Sbjct: 363 VGRALPQIEVKIALPGTSEEVPRGQQ--GELCTRGYHVMKGYYKNEEATNEVIDEDGWLH 420

Query: 421 TGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGE 480
           TGD+  M  DGY++I  R KD+II GGEN+   E+E +LY+HP IL+A VV  PDE +GE
Sbjct: 421 TGDLAEMDHDGYVKITGRLKDMIIRGGENVYPKEIEDVLYTHPAILDAQVVGIPDETYGE 480

Query: 481 TPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRDM 540
              AF+ LK+G  K  + + +  YC+S++ RY +PK     +E P T++GK+QKF L+  
Sbjct: 481 EAAAFIRLKQG--KSVSIETLTSYCQSQMARYKIPKYFFITDEYPMTASGKIQKFRLKKQ 538

Query: 541 A 541
           A
Sbjct: 539 A 539


Lambda     K      H
   0.319    0.135    0.412 

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: 733
Number of extensions: 45
Number of successful extensions: 5
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: 556
Length of database: 545
Length adjustment: 36
Effective length of query: 520
Effective length of database: 509
Effective search space:   264680
Effective search space used:   264680
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: 53 (25.0 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