GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Williamsia sterculiae CPCC 203464

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_076478048.1 BW971_RS07615 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_900156495.1:WP_076478048.1
          Length = 462

 Score =  207 bits (527), Expect = 5e-58
 Identities = 140/417 (33%), Positives = 217/417 (52%), Gaps = 30/417 (7%)

Query: 21  QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80
           +I P+    +    VWD +GR  LDF+  +   N GH HP+V+AA++ Q  KL     Q 
Sbjct: 43  EISPMGITASAGSYVWDGDGRRLLDFSSMLVNTNIGHQHPRVIAAIQRQAAKLCTVAPQY 102

Query: 81  LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140
            A +   E   ++ ++ PGD   K      G++A E+AV++AR  T R   +    +YHG
Sbjct: 103 -ANDVRSEAARLIAERTPGDL-DKIFFTNGGADANEHAVRMARLHTGRRKVLTRYRSYHG 160

Query: 141 RTHYTLALTGKVN--PYSAGMGLMPGHVYRALYPCPLHGISEDD----AIASIHRIFKND 194
            T   + LTG     P   G   +       LY    H  +E+     A+  +  + + +
Sbjct: 161 GTDTAINLTGDPRRWPNDHGDSGVVHFFGPFLYRSRFHAETEEQECARALDHLDEVIRME 220

Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254
             P  IAAIV+E + G  G     P +++ +R LCD +GI+ IADEV +G GR+GT F++
Sbjct: 221 G-PSTIAAIVLETIPGTAGIMIPPPGYLRGVRELCDRYGIVYIADEVMAGFGRSGTWFSV 279

Query: 255 EQMGVAPDLTTFAKSIAGGF-PLAGVTGRAEVMDAV----APGGLGGTYAGNPIACVAAL 309
           + +GV PDL TFAK +  G+ PL GV   A +         PGGL  TY+G+P+A  AA+
Sbjct: 280 DLVGVTPDLLTFAKGVNSGYVPLGGVAISAAIAATFDHRPYPGGL--TYSGHPLATAAAV 337

Query: 310 EVLKVFEQENLLQKANDLG-QKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKP 368
             +     E+++  A+ +G + +  GL  +A++HP +G+VRG G   A+EL  D    +P
Sbjct: 338 ATITAMADEDVVGNASRIGAEVIGPGLAELADRHPSVGEVRGCGVFWALELVRDRTTREP 397

Query: 369 DAKLTA------EIVARARDKGLILLSCGPYYNVLRILV--PLTIEDAQIRQGLEII 417
            A   A      ++VA  R  GL+     P+ NV RI V  P T+   ++R+GL ++
Sbjct: 398 LAPYGASSAAMNDVVAACRSGGLL-----PFANVNRIHVVPPCTVTAEEVREGLTVL 449


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: 564
Number of extensions: 29
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: 462
Length adjustment: 32
Effective length of query: 394
Effective length of database: 430
Effective search space:   169420
Effective search space used:   169420
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