GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Azospirillum brasilense Sp245

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 AZOBR_RS27880 AZOBR_RS27880 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS27880 AZOBR_RS27880
           4-aminobutyrate aminotransferase
          Length = 438

 Score =  168 bits (426), Expect = 3e-46
 Identities = 122/397 (30%), Positives = 200/397 (50%), Gaps = 21/397 (5%)

Query: 24  PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLS-HTCFQVLA 82
           PI   R E   ++D EG  YLD    +A  + GH  P+VV A+  Q   L+ HT +    
Sbjct: 41  PIHVVRGEGSSLYDAEGNRYLDAYNNVA--SVGHSRPEVVEAMARQAAVLNTHTRYLT-- 96

Query: 83  YEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRT 142
            +  L+  E    + P + +   +L  TGSEA + A+++AR  T  +G +    AYHG T
Sbjct: 97  -DGILDFAEAFLAEFPAELSH-LMLTCTGSEANDLALRVARVHTGGTGVVIAHNAYHGVT 154

Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKN---DAAPED 199
               +   +++P S G  +  G   R +     + + E +  A+  R  +    D   + 
Sbjct: 155 ----SALAEMSP-SLGAAVKLGDHVRVVPAPDGYRMPEAEVGAAFARSVEEAIADLREKG 209

Query: 200 I--AAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGT-LFAMEQ 256
           I  AA++++ +    G +     F+     +  + G + IADEVQ G GR GT ++   +
Sbjct: 210 ITPAALLVDTIFSSSGVFTDPAGFLAPAVEVMRKAGGVFIADEVQPGFGRLGTHMWGFAR 269

Query: 257 MGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGG-LGGTYAGNPIACVAALEVLKVF 315
            G+ PD+ T  K +  G P+AG   R EV++A         T+ GNP++C  AL VL+V 
Sbjct: 270 HGLVPDIVTVGKPMGNGHPVAGAVFRPEVIEAFGKSQRYFNTFGGNPVSCAVALAVLRVI 329

Query: 316 EQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAE 375
           +++ L + A  +G ++ DGL A+A KH  IGDVRG G  I +E+  D     P ++ TA 
Sbjct: 330 KEDRLQENALTVGTEMIDGLRALAAKHELIGDVRGSGLFIGVEMVRDRKLKTPASEETAR 389

Query: 376 IVARARDKGLILLSCGPYYNVLRILVPLTI--EDAQI 410
           +V   R + +++ + G   ++L+I  PL    EDA++
Sbjct: 390 VVNGMRQRRVLISATGQEGHILKIRPPLVFSSEDAKL 426


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: 472
Number of extensions: 27
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: 438
Length adjustment: 32
Effective length of query: 394
Effective length of database: 406
Effective search space:   159964
Effective search space used:   159964
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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