GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Sinorhizobium meliloti 1021

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate SMc02413 SMc02413 aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Smeli:SMc02413
          Length = 437

 Score =  241 bits (615), Expect = 3e-68
 Identities = 141/408 (34%), Positives = 214/408 (52%), Gaps = 15/408 (3%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P  +  G G  +   DG    DF++  G  ++GHSHP + EA+ +        S      
Sbjct: 22  PQAVVGGSGAYLTADDGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSAN 81

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
           E  ++LAEKL+ L P     +V +G+SG++ANE   ++V   TGR + LAF+ A+HG T 
Sbjct: 82  EACVLLAEKLLSLVPERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGT- 140

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
            + S+  S    Q G      G+T +PYPN Y           P+   +  L  +E    
Sbjct: 141 -IGSMGVSGHPAQQG--SRAEGLTLVPYPNSY-------AAGSPEAARDAALAHLERLFA 190

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
             VPP E+ A F EPIQ +GG +VPP GFFKA++     +GIL+  DEV++G+GR+G+F 
Sbjct: 191 TEVPPEEVAAFFIEPIQSDGGMLVPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFN 250

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAIAAGIEVVE 336
           A EH G+EPD++ FGK +GGGLP++ V+    I          T  GNPV  AA + V++
Sbjct: 251 AFEHSGIEPDIVVFGKGLGGGLPISAVVGPEAIMNHSVAFSLQTVHGNPVCAAAALAVLQ 310

Query: 337 IVK--ELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELR 394
            ++   L+ +    G  L + L+    ++ +IGD RG GLA  +E+V    ++E      
Sbjct: 311 TIERDHLILNADRSGKVLREALDRLTARHTLIGDVRGRGLALGIELVTDPASREPASRQA 370

Query: 395 DRIVKESAKRGLVL--LGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440
              V  + + GLVL  +G   N +   PPL +T  E +  + +  +AL
Sbjct: 371 ALTVYRAFQLGLVLYYVGVQSNVLELTPPLTLTPAEAESGVAMLGQAL 418


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: 489
Number of extensions: 30
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: 437
Length adjustment: 32
Effective length of query: 413
Effective length of database: 405
Effective search space:   167265
Effective search space used:   167265
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