GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Shewanella sp. ANA-3

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 7025922 Shewana3_3071 glutamate-1-semialdehyde aminotransferase (RefSeq)

Query= SwissProt::P22256
         (426 letters)



>lcl|FitnessBrowser__ANA3:7025922 Shewana3_3071
           glutamate-1-semialdehyde aminotransferase (RefSeq)
          Length = 430

 Score =  163 bits (412), Expect = 1e-44
 Identities = 113/362 (31%), Positives = 175/362 (48%), Gaps = 40/362 (11%)

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

Query: 52  VLNTGHLHPKVVAAVEAQLKKLSHTCFQVLA-YEPYLELCEIMNQKVPGDFAKKTLLVTT 110
            +  GH HPK+  AV A +    H      A  E  +++ E +   VP    ++  +V++
Sbjct: 61  PMILGHNHPKIREAVLAAV----HNGLSFGAPTELEVQMAEKVIAMVPS--IEQVRMVSS 114

Query: 111 GSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPG------ 164
           G+EA  +A+++AR  T R   + F G YHG     L   G     + G    PG      
Sbjct: 115 GTEATMSAIRLARGFTNRDKILKFEGCYHGHADCLLVKAGS-GALTLGQPSSPGIPEDFA 173

Query: 165 -HVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQ 223
            H   A+Y       ++ D++ S+   +     P +I+ I+IEPV G        P F++
Sbjct: 174 KHTLTAVY-------NDLDSVRSLFEQY-----PTEISCIIIEPVAGNMNCIPPIPGFLE 221

Query: 224 RLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRA 283
            LRA+CDE G +LI DEV +G  R     A    GV PDLTT  K I GG P+    GR 
Sbjct: 222 GLRAMCDEFGALLIIDEVMTGF-RVSRSGAQGHYGVTPDLTTLGKVIGGGMPVGAFGGRK 280

Query: 284 EVMDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAE 340
           EVM  +AP G     GT +GNPIA  A L  ++   +E L +  +   +++ +G  A A+
Sbjct: 281 EVMQFIAPTGPVYQAGTLSGNPIAMSAGLAQMEALCEEGLYEALSAKTKRIAEGFKAAAD 340

Query: 341 KH 342
           KH
Sbjct: 341 KH 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: 483
Number of extensions: 25
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: 430
Length adjustment: 32
Effective length of query: 394
Effective length of database: 398
Effective search space:   156812
Effective search space used:   156812
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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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