GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Shewanella amazonensis SB2B

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 6938533 Sama_2636 4-aminobutyrate aminotransferase (RefSeq)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__SB2B:6938533
          Length = 425

 Score =  260 bits (665), Expect = 5e-74
 Identities = 151/413 (36%), Positives = 218/413 (52%), Gaps = 19/413 (4%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P+  ER E   V+DV+G  + DFA G+ V+N GH HP+V  A+ +Q EKF+H       Y
Sbjct: 25  PVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGY 84

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
           E+ + + EKL +L PGD  +K     SG+EA E A+K+ +  T R   +AF   +HGRT 
Sbjct: 85  ESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAYTKRAGVIAFTSGYHGRTM 144

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
           A L+LT        G       V    +P        + G  E D + +     IE    
Sbjct: 145 AALALTGKVAPYSKGMGLMQANVFRAEFP------CALHGVSEDDAMAS-----IERIFK 193

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
               P +I AI  EP+QGEGG+     GF K L++  D  GI+L  DEVQ G GRTG F+
Sbjct: 194 NDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFF 253

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335
           A+E  GV  D+  F K+I GG PL+G+  RA++     PG    T+GG+P+A AA + V+
Sbjct: 254 AMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVI 313

Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393
           E+ +E  LL     +G  +   + E   +Y  I + RGLG   A+E++   E  +  PE 
Sbjct: 314 EVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELM---ENGKPAPEY 370

Query: 394 RDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444
             +++ E+  RGL+LL CG   N +R + P+    E+I   +EI  E  +A L
Sbjct: 371 CPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423


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: 479
Number of extensions: 24
Number of successful extensions: 6
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: 425
Length adjustment: 32
Effective length of query: 413
Effective length of database: 393
Effective search space:   162309
Effective search space used:   162309
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 17 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