GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Amantichitinum ursilacus IGB-41

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_053937789.1 WG78_RS10575 long-chain-fatty-acid--CoA ligase FadD

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



>NCBI__GCF_001294205.1:WP_053937789.1
          Length = 554

 Score =  141 bits (356), Expect = 6e-38
 Identities = 115/375 (30%), Positives = 179/375 (47%), Gaps = 49/375 (13%)

Query: 185 DPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW--GVPK--QPVYLWTLPMFH---- 236
           D   L YT GTT   KG +  HR I +  +     W  GV    + + +  LP++H    
Sbjct: 207 DLAFLQYTGGTTGVAKGAMLTHRNI-VANMQQAHAWIGGVVADGRELIVTALPLYHIFSL 265

Query: 237 -ANGWSYPWGMAAVGGTNICLRK-FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEP 294
            ANG  +      +G TN+ +    D       + ++ VT + G   + N L N P    
Sbjct: 266 TANGMIF----TKIGATNLLITNPRDIPGFIKELGKYPVTAITGVNTLFNALVNHPDFLK 321

Query: 295 LKTTVQIMTAGA----PPPSAVLFRTESLGFAVSHGYGLTETA-GLVVSCAWKKEWNHL- 348
           L  +   +T G       P A  ++  + G  +   YGLTET+   +++    +E+N + 
Sbjct: 322 LDFSSWKLTLGGGMAVQQPVADKWKKVT-GVTLVEAYGLTETSPAAMINPMTLREYNGMI 380

Query: 349 ----PATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLK 404
               P+T+ A+++   G                  +V+  GS  GE+ ++G  VM GY +
Sbjct: 381 GLPVPSTD-AQIRGEDG------------------SVQPPGSA-GELFIKGPQVMKGYWQ 420

Query: 405 DPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPD 464
             + TAK + ADG+  TGDV +M P G+  I DR KD+++  G N+   EVE ++  HP 
Sbjct: 421 RADETAKVIGADGYLATGDVAIMSPTGFFRIADRKKDMVLVSGFNVYPNEVEDVVARHPG 480

Query: 465 ILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEEL 524
           +LE A V  PD+  GE    FV  K       TE  ++ YCR +L  Y VP+ V F++ L
Sbjct: 481 VLEVACVGVPDDKSGEAVKIFVVRKDPTL---TEAALIAYCREQLTNYKVPRKVEFRDAL 537

Query: 525 PKTSTGKVQKFILRD 539
           PK++ GK+ +  LRD
Sbjct: 538 PKSNVGKILRRELRD 552


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: 707
Number of extensions: 34
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 556
Length of database: 554
Length adjustment: 36
Effective length of query: 520
Effective length of database: 518
Effective search space:   269360
Effective search space used:   269360
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.

Links

Downloads

Related tools

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