GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Shewanella loihica PV-4

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 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__PV4:5210744
          Length = 426

 Score =  463 bits (1191), Expect = e-135
 Identities = 230/421 (54%), Positives = 294/421 (69%), Gaps = 1/421 (0%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           SN EL  R+ QAI RG G  +P++ +RA N  +WDVEG+ Y+DF  GIAV NTGH HPKV
Sbjct: 2   SNAELQARKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKV 61

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           VAAV+AQL   SHTC  V  YE  + L E +N+  PG   KK + VTTG+EAVEN VKIA
Sbjct: 62  VAAVKAQLDNFSHTCVMVNPYESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIA 121

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RA T R G IAF+G +HGRT+ T+ALTGK+ PY    G   G ++ A YP   HG+S  D
Sbjct: 122 RAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKD 181

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           ++ +I  +FK D AP D+AAIV+EPVQGEGGFYA+ P F+Q LRALCD+HGI+L+ DE+Q
Sbjct: 182 SLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQ 241

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           +G GRTG +F+ E  GV PDL T AK IAGGFPLA V G++E+MDA  PGGLGGTY G+P
Sbjct: 242 TGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSP 301

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIELFE 361
           + CVAAL VL+V ++E L+++A  +G      L A+ E++P+ IG+VR  GAMIA+EL  
Sbjct: 302 VGCVAALAVLEVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVI 361

Query: 362 DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCF 421
           DGD  +P+  LT  I+A A   GL+LL+CG Y NV+R L  LTI D  + +GL      F
Sbjct: 362 DGDIEQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLF 421

Query: 422 D 422
           +
Sbjct: 422 E 422


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: 566
Number of extensions: 19
Number of successful extensions: 2
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