GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Dinoroseobacter shibae DFL-12

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate 3610820 Dshi_4206 aminotransferase class IV (RefSeq)

Query= curated2:O29329
         (290 letters)



>FitnessBrowser__Dino:3610820
          Length = 307

 Score =  160 bits (405), Expect = 3e-44
 Identities = 91/268 (33%), Positives = 149/268 (55%), Gaps = 12/268 (4%)

Query: 4   VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63
           +Y++G     +EA VS++D GF+ GDG++EG+R Y+G    L +H+DR Y+S KA+ L++
Sbjct: 20  IYINGALKHRSEAMVSVYDSGFMLGDGMWEGLRLYDGVWAFLDDHMDRFYNSCKAVSLDV 79

Query: 64  PITKEEFMEIILETLRKNNLR-DAYIRPIVTRGIGDLGLDPRKCQNPSI------IVITK 116
            + +    + +  T R N++  D + R ++TRG+       R  Q+P++      +VI  
Sbjct: 80  GMDRAALFDALETTRRANDMHTDVHCRLMLTRGV-----KVRPFQHPALSRSGPTLVILM 134

Query: 117 PWGKLYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLD 176
              K    L++KG+   TV   R    +      S + LN ++A ++A   G DEA+ LD
Sbjct: 135 EHSKPVDRLHDKGIRLATVPQVRGLPMSQDAKYNSHSKLNCVIACLQAEQAGADEALMLD 194

Query: 177 RNGYVSEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLY 236
            +G+V+  +  N F+V+ G + T      + G+TR+ VI++    GIP +E N  LY+  
Sbjct: 195 PHGFVNTTNACNFFIVRKGEVWTSTGDYCMNGVTRQKVIDLCRANGIPVREKNYSLYEAI 254

Query: 237 TADEVFVTGTAAEIAPIVVIDGRKIGDG 264
            ADE F+TGT     P+  IDG+ IGDG
Sbjct: 255 GADEAFLTGTFGAQTPVASIDGKPIGDG 282


Lambda     K      H
   0.319    0.142    0.409 

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: 262
Number of extensions: 15
Number of successful extensions: 2
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: 290
Length of database: 307
Length adjustment: 27
Effective length of query: 263
Effective length of database: 280
Effective search space:    73640
Effective search space used:    73640
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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