GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Williamsia sterculiae CPCC 203464

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_900156495.1:WP_076476008.1
          Length = 452

 Score =  258 bits (660), Expect = 2e-73
 Identities = 161/443 (36%), Positives = 236/443 (53%), Gaps = 24/443 (5%)

Query: 7   VKELPGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVI 66
           V  LPGP++  + +R  +  A+       +PI     +G  + DVDGN   D  SG+ V 
Sbjct: 16  VTPLPGPESSALAKR--RAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGSGIAVT 73

Query: 67  NVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAE 126
            VG S+P V +A+  QA  FTH       YE  + +AEKL EL PGD E++ V  NSGAE
Sbjct: 74  GVGASNPAVADAVAAQAHHFTHTCFMVTPYEGYVAVAEKLNELTPGDHEKRSVLFNSGAE 133

Query: 127 ANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPN 186
           A E A+K+ +  TGR   +AF HA+HGRT   ++LTA     +  F P  P +  +P   
Sbjct: 134 AVENAVKVARLATGRDAIVAFDHAYHGRTNLTMALTAKTQPYKYNFGPFAPEIYRMPMSY 193

Query: 187 PYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFF 246
           PYR+  G DG         R +  IE      +    +  +  EPIQGEGG++VP  GF 
Sbjct: 194 PYRDDLGTDGV----SAAKRAIRQIE----TQIGGEAVAGLLIEPIQGEGGFIVPAPGFL 245

Query: 247 KALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHR 306
             L ++A + G++   DEVQ G  RTG ++A E  G+ PD++   K I GG+PL+ +  R
Sbjct: 246 TTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPDIVTTAKGIAGGMPLSAITGR 305

Query: 307 ADITFDK--PGRHATTFGGNPVAIAAGIEVVEIVKEL-----LPHVQEVGDYLHKYLEEF 359
           AD+  DK  PG    T+GGNPVA AA +  +  ++EL       H++E+       L   
Sbjct: 306 ADL-LDKVHPGGLGGTYGGNPVACAAALATIAEMEELDLNARAHHIEEIA---LPRLRTL 361

Query: 360 KEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLL--GCGDNSIR 417
            +  +VIGD RG G   A+EIV+   T    P L  ++   + + G+V+L  G   N IR
Sbjct: 362 ADDLDVIGDVRGRGAMLAIEIVE-PGTDTPAPALAKKVAAAALEAGVVILVTGTFGNVIR 420

Query: 418 FIPPLIVTKEEIDVAMEIFEEAL 440
            +PPL++  E +   +++ E++L
Sbjct: 421 LLPPLVIDDETLVDGIDVLEQSL 443


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: 531
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: 452
Length adjustment: 33
Effective length of query: 412
Effective length of database: 419
Effective search space:   172628
Effective search space used:   172628
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 Sep 24 2021. The underlying query database was built on Sep 17 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