GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhodanobacter denitrificans 2APBS1

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_007509924.1 R2APBS1_RS07500 long-chain fatty acid--CoA ligase

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



>NCBI__GCF_000230695.2:WP_007509924.1
          Length = 561

 Score =  148 bits (374), Expect = 5e-40
 Identities = 143/517 (27%), Positives = 218/517 (42%), Gaps = 68/517 (13%)

Query: 59  LGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFV- 117
           L +  G  ++++ PNV Q     F    AG ++   N    AR +   L  S ++ I V 
Sbjct: 71  LKLGKGDRIALMMPNVLQYPIALFGALRAGLVVVNTNPMYTARELKHQLEDSGARAIVVL 130

Query: 118 -------DHLSRDLILEAIAL--------FPKQAPVPRLVFMADESESGNSSELGKEFFC 162
                   H+  +  ++ +          FPK A +  ++    +            F  
Sbjct: 131 DNFAATLQHVVAETHVQHVITTGIGDLLGFPKGALINFVLKHVKKMVPAFDLPQAVRF-- 188

Query: 163 SYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGV 222
             +D + RG       +     D   L YT GTT   KG +  H  +    + +    G 
Sbjct: 189 --RDALARGAAHPLQPVTLGHDDIAFLQYTGGTTGVAKGAMLTHGNMVANMLQAAAWIGT 246

Query: 223 ----PKQPVYLWTLPMFH-----ANGWSYPWGMAAVGGTN-ICLRKFDSEIIYDMIKRHG 272
               P + V +  LP++H     ANG  +      +GG N +     D       +++ G
Sbjct: 247 ELVTPGEEVIITALPLYHIFSLTANGLVF----MRLGGLNWLITNPRDMPGFVKELRKSG 302

Query: 273 VTHMCGAPVVLNMLSNAPGSEPLKTTVQIMTAGA--PPPSAVLFRTESL-GFAVSHGYGL 329
            T + G   + N L N PG   L  +   +T G       AV  R + + G  ++  YGL
Sbjct: 303 FTALTGVNTLFNGLLNTPGFSELDFSKLHLTLGGGMAVQRAVAERWKKVTGCTLAEAYGL 362

Query: 330 TETAGLV-VSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAV-KRDGST 387
           TET+  V ++    KE+N                       I +  P T  A+   DG  
Sbjct: 363 TETSPAVCINPLDLKEYNG---------------------SIGLPVPSTNVAIWSEDGKP 401

Query: 388 L-----GEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDV 442
           L     GE+++ G  VM GY   P+ TAK + ADGW +TGD+  M  +GY  I DR KD+
Sbjct: 402 LPVGEVGELMVHGPQVMKGYWNRPDETAKVLGADGWLHTGDIAKMDVNGYFYIVDRKKDM 461

Query: 443 IISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIV 502
           I+  G N+   EVE  + +HP +LE A V  PDE  GE    FV  K       TE+ + 
Sbjct: 462 ILVSGFNVYPNEVEDAVMAHPGVLEVAAVGVPDEHSGEVVKLFVVRK---DPNLTEEALK 518

Query: 503 EYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539
           ++CR  L  Y  PK + F++ LPK++ GK+ +  LRD
Sbjct: 519 QFCRENLTGYKRPKLIEFRDSLPKSNVGKILRRELRD 555


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: 736
Number of extensions: 33
Number of successful extensions: 3
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: 561
Length adjustment: 36
Effective length of query: 520
Effective length of database: 525
Effective search space:   273000
Effective search space used:   273000
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