GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Pseudomonas litoralis 2SM5

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_900105005.1:WP_090271605.1
          Length = 417

 Score =  235 bits (600), Expect = 2e-66
 Identities = 133/408 (32%), Positives = 217/408 (53%), Gaps = 14/408 (3%)

Query: 38  IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97
           +  ERGEG  +   DG  + DF +G+GV + GH HP VV A ++Q  K  H   T   ++
Sbjct: 14  VCAERGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTTVTHQ 73

Query: 98  NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157
             + LAE+L+   P  I+  V + N+G+EA E A++L ++ T R   + F   FHGRT  
Sbjct: 74  PMLDLAERLVGKMPDGID-SVAFSNAGSEAVEMALRLARHATRRANVIVFNGGFHGRTMG 132

Query: 158 VLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR 217
             S+T S    ++ + P M GV   P+P+ +R  W        +E T   L  ++  +  
Sbjct: 133 AASMTTSGTKVRNAYHPMMAGVVVAPFPHSWRYGWS------EEEATRFCLAELDHILKT 186

Query: 218 HVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWA 277
              P +  A+  EP+QGE GY      F + L +   ++GILL  DE+Q G GR+GKFW+
Sbjct: 187 QTAPEDTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWS 246

Query: 278 IEHFGVEPDLIQFGKAIGGGLPLAGV-IHRADITFDKPGRHATTFGGNPVAIAAGIEVVE 336
            +HFG+ PD++   K +  G PL+ +   +  +     G    T+G N V+ AA +  + 
Sbjct: 247 HQHFGITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLR 306

Query: 337 IV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELR 394
           ++  + L+ +    G  L  +L+  +++Y  + D RG GL   +EI +S +  +   +L 
Sbjct: 307 VMDNENLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPD--KPLADLA 364

Query: 395 DRIVKESAKRGLVLLGCGDNS--IRFIPPLIVTKEEIDVAMEIFEEAL 440
             +   S + GL+LL CG +S  IR++PPL+V++ E+D A++ F   L
Sbjct: 365 ASLTTASEEEGLLLLRCGTDSQIIRWLPPLVVSEAEVDDAVQRFTRVL 412


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: 411
Number of extensions: 18
Number of successful extensions: 5
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: 417
Length adjustment: 32
Effective length of query: 413
Effective length of database: 385
Effective search space:   159005
Effective search space used:   159005
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