GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Acidovorax caeni R-24608

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 WP_054255500.1 BN2503_RS04745 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_001298675.1:WP_054255500.1
          Length = 436

 Score =  155 bits (393), Expect = 2e-42
 Identities = 121/391 (30%), Positives = 176/391 (45%), Gaps = 37/391 (9%)

Query: 4   NKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVLN 54
           N  L +R    IP GV             P F  RA+   +WD  G+ ++D+ G    + 
Sbjct: 8   NLSLFERAKALIPGGVNSPVRAFRAVGGTPRFIARAQGAYMWDANGQRFIDYIGSWGPMI 67

Query: 55  TGHLHPKVVAAVE-AQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSE 113
            GH HP V+ AV+ A L+  S         E  +EL E + + VP    +   LV++G+E
Sbjct: 68  LGHGHPAVLEAVQKAALEGFSFGA----PTEREVELAEEIIRHVPS--MEMIRLVSSGTE 121

Query: 114 AVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMP-GHVYRALYP 172
           A  +A+++AR AT RS  I F+G YHG     L          AG GL   GH   A  P
Sbjct: 122 AGMSAIRLARGATGRSKIIKFNGCYHGHADSLLV--------KAGSGLATFGHATSAGVP 173

Query: 173 CPLHG---ISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALC 229
             +     + E + +A +   F      +++A +++EP+ G   F  +S  FM+R R LC
Sbjct: 174 AEVVQHTLVLEYNDVAQLEEAFALHG--KEVACVIMEPIAGNMNFVRASVPFMRRARELC 231

Query: 230 DEHGIMLIADEVQS----GAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEV 285
            +HG +L+ DEV +    G G    L+A +  G APDLT   K I GG PLA   G   +
Sbjct: 232 TQHGALLVIDEVMTGFRVGLGSAQGLYAQQIPGFAPDLTVLGKVIGGGMPLAAFGGPRAI 291

Query: 286 MDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKH 342
           M+ +AP G     GT +GNP+A    L  L+   +    ++     + L DGL   A+  
Sbjct: 292 MEQLAPLGPVYQAGTLSGNPVATACGLATLREIAKPGFYEQLAARTRALIDGLAGAAQAE 351

Query: 343 PEIGDVRGLGAMIAIELFEDGDHNKPDAKLT 373
                    G M    L      N P+   T
Sbjct: 352 GVAFCADSEGGMFGFFLLPQLPQNYPEVLKT 382


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: 23
Number of successful extensions: 5
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: 436
Length adjustment: 32
Effective length of query: 394
Effective length of database: 404
Effective search space:   159176
Effective search space used:   159176
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 24 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