GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella loihica PV-4

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate 5208501 Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__PV4:5208501
          Length = 428

 Score =  164 bits (415), Expect = 5e-45
 Identities = 115/365 (31%), Positives = 172/365 (47%), Gaps = 46/365 (12%)

Query: 1   MNSNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIA 51
           M  ++ L ++  + IP GV             P F ++A+   ++D +G+ Y+D+ G   
Sbjct: 1   MTRSETLFEQAKKTIPGGVNSPVRAFNGVGGSPRFIEKADGAYIYDADGKAYIDYVGSWG 60

Query: 52  VLNTGHLHPK----VVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLL 107
            +  GH HPK    V+ AVE  L   + T  +V   E  +E+   M Q           +
Sbjct: 61  PMILGHNHPKIRQAVLDAVENGLSFGAPTELEVRMAEKVIEMVPSMEQ---------VRM 111

Query: 108 VTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPG--- 164
           V++G+EA  +A+++AR  T R   + F G YHG     L   G     + G    PG   
Sbjct: 112 VSSGTEATMSAIRLARGFTNRDKILKFEGCYHGHADCLLVKAGS-GALTLGQPSSPGIPE 170

Query: 165 ----HVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPA 220
               H   A+Y          + + S+  +F+    PE+IA I++EPV G        P 
Sbjct: 171 DFAKHTLTAVY----------NELESVKTLFEQ--YPEEIACIILEPVAGNMNCIPPIPG 218

Query: 221 FMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVT 280
           F++ LRALCD++G +LI DEV +G  R     A    G+ PDLTT  K I GG P+    
Sbjct: 219 FLEGLRALCDQYGALLIIDEVMTGF-RVSKSGAQGHYGITPDLTTLGKVIGGGMPVGAFG 277

Query: 281 GRAEVMDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLA 337
           GR EVM  +AP G     GT +GNPIA  A L  ++    E L ++     +++ +G  A
Sbjct: 278 GRKEVMQFIAPTGPVYQAGTLSGNPIAMSAGLAQMEELCAEGLYEELAAKTKRIAEGFKA 337

Query: 338 IAEKH 342
            A KH
Sbjct: 338 AANKH 342


Lambda     K      H
   0.320    0.137    0.401 

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: 485
Number of extensions: 22
Number of successful extensions: 6
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: 426
Length of database: 428
Length adjustment: 32
Effective length of query: 394
Effective length of database: 396
Effective search space:   156024
Effective search space used:   156024
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 (21.8 bits)
S2: 51 (24.3 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