GapMind for catabolism of small carbon sources

 

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

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__PV4:5210744
          Length = 426

 Score =  268 bits (686), Expect = 2e-76
 Identities = 148/397 (37%), Positives = 224/397 (56%), Gaps = 17/397 (4%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P+ +ER     ++DV+G  + DF +G+ V N GHSHP+VV A+K Q + F+H  +    Y
Sbjct: 23  PVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTCVMVNPY 82

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
           E+A+ LAE+L  +APG  ++K ++  +GAEA E  +K+ +  TGR+  +AF   FHGRT 
Sbjct: 83  ESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRGVIAFNGGFHGRTN 142

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
             ++LT      +  F P    + H PYP  +      D            L  IE    
Sbjct: 143 LTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDS-----------LKAIEHLFK 191

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
             + P ++ AI  EP+QGEGG+   P  F +AL+   D++GI+L  DE+Q G GRTGK +
Sbjct: 192 VDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMF 251

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335
           + EH GVEPDL+   K I GG PLA V+ +++I     PG    T+GG+PV   A + V+
Sbjct: 252 SCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVL 311

Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQAVEIVKSKETKEKYPE 392
           E+++E  L+    ++GD  ++ L   KE+Y ++IG+ R  G   A+E+V   + ++    
Sbjct: 312 EVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVIDGDIEQPNTA 371

Query: 393 LRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKE 427
           L   I+  +A  GLVLL CG   N IRF+P L ++ E
Sbjct: 372 LTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDE 408


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: 515
Number of extensions: 25
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: 426
Length adjustment: 32
Effective length of query: 413
Effective length of database: 394
Effective search space:   162722
Effective search space used:   162722
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.

Links

Downloads

Related tools

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