GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Pseudomonas stutzeri RCH2

Align 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__psRCH2:GFF3586
          Length = 426

 Score =  646 bits (1667), Expect = 0.0
 Identities = 317/421 (75%), Positives = 362/421 (85%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           +N+ LMQRR  A+PRGVGQIHPIFAD A+N  V DVEGRE++DFAGGIAVLNTGHLHPK+
Sbjct: 4   TNESLMQRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKI 63

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           + AVE QL KL+HTCFQVLAYEPY+ELCE +N +VPGDFAKKTLLVTTGSEAVENAVKIA
Sbjct: 64  IKAVEDQLHKLTHTCFQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIA 123

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RAAT R+G IAF+GAYHGRT  TL LTGKV PYSAGMGLMPG ++RALYPC ++G+S DD
Sbjct: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVSVDD 183

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           +IASI RIFKNDA P DIAAI+IEPVQGEGGF  +   FM RLRALCDEHGI+LIADEVQ
Sbjct: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIADEVQ 243

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           +GAGRTGT FAMEQMGV  DLTTFAKS+ GGFP+AGV G+AE+MDA+APGGLGGTYAGNP
Sbjct: 244 TGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNP 303

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
           ++C AAL VL+VFE+E LL +   + ++L  GL AI  KH EIG+VRGLGAMIAIELFED
Sbjct: 304 LSCAAALAVLEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIELFED 363

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
           GDH +P A LT++IVARARDKGLILLSCG YYNVLR+LVPLT ED  + +GL II +CFD
Sbjct: 364 GDHARPAAALTSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGECFD 423

Query: 423 E 423
           E
Sbjct: 424 E 424


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: 701
Number of extensions: 22
Number of successful extensions: 1
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: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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 Aug 03 2021. The underlying query database was built on Aug 03 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