GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02413 SMc02413 aminotransferase
          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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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