GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Crocosphaera subtropica ATCC 51142

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_009546068.1 CCE_RS03960 1,4-dihydroxy-2-naphthoyl-CoA synthase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_000017845.1:WP_009546068.1
          Length = 277

 Score =  113 bits (282), Expect = 5e-30
 Identities = 84/265 (31%), Positives = 129/265 (48%), Gaps = 15/265 (5%)

Query: 3   YENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS----- 57
           YE+IL      +  +T+NRP   NA     + EL  A  +   D +IG I++TG+     
Sbjct: 11  YEDILYHKADGIAKITINRPHKRNAFRPKTVFELYDAFCDAREDSSIGVILLTGAGPHTD 70

Query: 58  -EKAFAAGADIGMMSTYTYMD---VYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCEL 113
            + AF +G D  +     Y+D   + + + +      +RS+ K +IA VAG+A+GGG  L
Sbjct: 71  GKYAFCSGGDQSVRGQAGYVDDAGIPRLNVLDLQ-RLIRSMPKVVIALVAGYAIGGGHVL 129

Query: 114 AMMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAER 173
            ++CD+  AAD A FGQ   K+G   G  G   L R + + KA ++    R  +A +A  
Sbjct: 130 HVICDLTIAADNAVFGQTGPKVGSFDGGFGASYLARIIGQKKAREIWFLCRQYNAEQALE 189

Query: 174 AGLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAY--ETTLAEGVHFERRLF 231
            GLV+ V+P   L  E +  A  I      A+  +K + N     +  L E       L+
Sbjct: 190 MGLVNCVVPVEQLETEGVQWAKEILSKSPIAIRCLKAAFNADCDGQAGLQELAGNATLLY 249

Query: 232 HSLFATEDQKEGMAAFVEKRKPVFK 256
              + TE+  EG  AF+EKR P F+
Sbjct: 250 ---YMTEEGAEGKQAFLEKRPPNFR 271


Lambda     K      H
   0.321    0.134    0.380 

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: 157
Number of extensions: 10
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: 258
Length of database: 277
Length adjustment: 25
Effective length of query: 233
Effective length of database: 252
Effective search space:    58716
Effective search space used:    58716
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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