GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingobium czechense LL01

Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_066599219.1 V473_RS00565 long-chain fatty acid--CoA ligase

Query= metacyc::MONOMER-20124
         (573 letters)



>NCBI__GCF_001046645.1:WP_066599219.1
          Length = 503

 Score =  191 bits (485), Expect = 6e-53
 Identities = 156/532 (29%), Positives = 255/532 (47%), Gaps = 42/532 (7%)

Query: 48  LERSSKAYRDNTSLVYGSVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIY 107
           L  S+  + D  ++++ + R T+        + A+ L   L I P   VA    N  +  
Sbjct: 7   LFESASRHCDKLAIIFENRRLTYGALRLEVERAAAGLQA-LDIGPSKRVAVMLENGLDFV 65

Query: 108 ELHFAVPMAGGILCTLNARNDSAMVSTLLAHSEAKLIFVEPQLLETARAALDLLAQKDIK 167
             ++A    G  + T++A    +  S +L  S A L+    ++ +TA+AA D    +  +
Sbjct: 66  VAYYATLATGASVVTVSALLTVSEASYVLKDSTADLLIGGGRVWDTAQAAADGAGLQAFQ 125

Query: 168 PPTLVLLTDSESFTSSSYDHYNHLLANGSDDFEIRRPKNEWDPISINYTSGTTARPKAVV 227
              L     +E  T                 +    P +  D   I YTSGTT +PK  +
Sbjct: 126 LADL-----AEGLT-----------------YICPTPPDGRDEAVIMYTSGTTGKPKGAI 163

Query: 228 YSHRGAYLNSIATVL--LHGMGTTSVYLWSVPMFHCNGW-CFPWGAAAQGATNICIRKVS 284
            +H    +N++ +V   +  +    V L  +P+FH +G  C        GAT + +R+ +
Sbjct: 164 LTHDNLTMNALVSVGQGMFNLSPEDVVLCCIPLFHASGQSCLLNTGLLAGATVVIMRQFA 223

Query: 285 PKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHTPLPHKVEVMTGGSPPPPKVIARME 344
            +A+ D + L KVT F   PT+   +++    N    LPH    ++GG+P P  V+  +E
Sbjct: 224 AQAVLDVMRLEKVTFFLGVPTMYVGLLSLVRPN-KAELPHWRVAVSGGAPIPVAVLEEVE 282

Query: 345 EMGFQVNHI--YGLTETCGPAANCVCKPEWDALQPEERYALKARQGLNHLAMEEMDVRDP 402
            + F+V+    YGLTET   A  C  +P+++        A+   Q    +A  E++ R  
Sbjct: 283 RL-FEVDIYEGYGLTETSPTA--CFNQPDFERRPGTIGKAIWGVQC--EVARIELEDR-- 335

Query: 403 VTMESVRADGATIGEVMFRGNTVMSGYFKDLKATEEAFEGGWFRSGDLGVKHEDGYIQLK 462
             +E + AD   +GE++ RG+ V +GY     AT      GWFR+GD+  K EDGY+++ 
Sbjct: 336 --IELLAAD--EVGELVVRGHNVFAGYLNQADATRACMVDGWFRTGDIATKDEDGYVRIV 391

Query: 463 DRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARPDKLWGETPCAFVTLKEGFDNDV 522
           DRKKD++I GG N+ + E+E VL +H A+  AAVV RPD L+GE   A V L       +
Sbjct: 392 DRKKDMIIRGGFNVYSREIEEVLSTHPAIALAAVVGRPDDLFGEEIVAVVQLHRDMAG-I 450

Query: 523 SADQIIKFCRDRLPHYMAPKTVVF-EELPKTSTGKIQKYILKEKAMAMGSLS 573
           S+  ++++ +  L  Y  P+  VF E +P   +GKI K  L E    + + S
Sbjct: 451 SSSDMVEWAKRHLAKYKYPREFVFVETIPLGPSGKILKRELAELVARLSTAS 502


Lambda     K      H
   0.318    0.133    0.408 

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: 633
Number of extensions: 44
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: 573
Length of database: 503
Length adjustment: 35
Effective length of query: 538
Effective length of database: 468
Effective search space:   251784
Effective search space used:   251784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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