GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Herbaspirillum autotrophicum IAM 14942

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_050461046.1 AKL27_RS02370 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_001189915.1:WP_050461046.1
          Length = 422

 Score =  258 bits (659), Expect = 3e-73
 Identities = 152/407 (37%), Positives = 221/407 (54%), Gaps = 17/407 (4%)

Query: 42  RGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAII 101
           R E   ++DV+G  + DFA+G+ V+N GH HP++V AIK+Q + FTH +     Y + + 
Sbjct: 28  RAENSELWDVEGRRYIDFAAGIAVLNTGHRHPKLVAAIKQQLDHFTHTAYQIVPYASYVE 87

Query: 102 LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSL 161
           LAE++  LAPG   +K    ++GAEA E A+K+ +  TGR   +AF   FHGRT   ++L
Sbjct: 88  LAERINTLAPGAFPKKTALFSTGAEAVENAIKIARAATGRAAVIAFSGGFHGRTMMGMAL 147

Query: 162 TASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPP 221
           T      + GF P    V H+P+P+              D  T   L  I+      V  
Sbjct: 148 TGKVVPYKVGFGPFPGDVYHVPFPSALH-----------DISTEDSLSAIQALFKSDVEA 196

Query: 222 HEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHF 281
             + AI  EP+QGEGG+   P      L++  DE+GILL  DEVQ G  RTGK +A+EH+
Sbjct: 197 KRVAAIIIEPVQGEGGFQAAPPELMHGLRRICDEHGILLIADEVQTGFARTGKLFAMEHY 256

Query: 282 GVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVKE 340
            V  DLI   K++ GG+PL+ V  R +I     PG    T+ GNP+A+A+ + V++++KE
Sbjct: 257 DVAADLITMAKSLAGGMPLSAVCGRTEIMDAPAPGGLGGTYAGNPLAVASALAVLDVIKE 316

Query: 341 --LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIV 398
             L+     +GD L   L E +     IG+ RG G   AVE VK   T E   +   R+ 
Sbjct: 317 EQLVERGARLGDQLKATLNELRGSVPAIGEIRGPGAMVAVEFVKPGST-EPDADFTKRVQ 375

Query: 399 KESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKAA 443
             + ++GL+LL CG   N IRF+ PL +    +D A+ I  + L+AA
Sbjct: 376 TLALQQGLLLLSCGTYGNVIRFLFPLTIQDAVMDEALAILRQVLRAA 422


Lambda     K      H
   0.320    0.141    0.418 

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: 491
Number of extensions: 24
Number of successful extensions: 4
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: 445
Length of database: 422
Length adjustment: 32
Effective length of query: 413
Effective length of database: 390
Effective search space:   161070
Effective search space used:   161070
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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