GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Herbaspirillum seropedicae SmR1

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 HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__HerbieS:HSERO_RS05420
          Length = 426

 Score =  469 bits (1206), Expect = e-137
 Identities = 231/417 (55%), Positives = 303/417 (72%), Gaps = 1/417 (0%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           +N+EL QR++ A PRGVG +   +A+RA N  +WDVEGR ++DFA GIAVLNTGH HPK+
Sbjct: 6   NNQELQQRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKL 65

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           + A+ AQ+ K +HT +Q++ Y  Y+EL E +N+  PG++ KKT   +TG+EAVENA+KIA
Sbjct: 66  LDAMRAQMDKFTHTAYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIA 125

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RA T R G IAF+G +HGRT   +ALTGKV PY  G G  PG V+ A YP  LHGI+ +D
Sbjct: 126 RAHTGRPGVIAFAGGFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSED 185

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           A+ ++  +FK+D   + +AAI++EPVQGEGGFYA+   FM+ LRALCDEHGI+LIADEVQ
Sbjct: 186 ALEAVKGLFKSDIEAKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQ 245

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           SG GRTG LFAME   V PDL T AKS+AGG PL+ V GRAE+MDA APGGLGGTYAGNP
Sbjct: 246 SGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNP 305

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
           +A  +AL VL V E+E L+ +   LG KL++ L  +    P+I +VRG+GAM+A+E F D
Sbjct: 306 LAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVE-FAD 364

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419
               KPDA+ T ++   A + GL+LL+CG Y NV+R L PLTI D  + + L I+++
Sbjct: 365 PATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAK 421


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: 609
Number of extensions: 24
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