GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Sinorhizobium meliloti 1021

Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate SMc00078 SMc00078 Leu/Ile/Val-binding protein

Query= TCDB::P0AD96
         (367 letters)



>lcl|FitnessBrowser__Smeli:SMc00078 SMc00078 Leu/Ile/Val-binding
           protein
          Length = 368

 Score =  293 bits (750), Expect = 5e-84
 Identities = 153/359 (42%), Positives = 228/359 (63%), Gaps = 9/359 (2%)

Query: 3   IKGKALLAGCIALAFSNMALAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGI 62
           + G AL A   ++AF+ +A A DI + V+  ++GPVA +G+Q   GAE AV  IN+ GG+
Sbjct: 6   LTGMALAA---SVAFAPLAHA-DITIGVITPLTGPVAAFGEQVKNGAEAAVEAINSAGGV 61

Query: 63  KGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITP 122
            G KL +   DDA +PKQAV+VAN++  +GI+YV+G + S ++ PASD+  + GILM+TP
Sbjct: 62  NGEKLVVKIVDDAGEPKQAVSVANQLAGEGIQYVVGPVLSGTSMPASDVLAENGILMVTP 121

Query: 123 AATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQ 182
            AT P+LT RG   +LRT G D  Q   AA Y+++  K +R+A++HDK  YG+GLA   +
Sbjct: 122 TATTPDLTTRGLWNVLRTCGRDDQQAVVAADYVVKNFKDKRVAVLHDKGAYGKGLADGFK 181

Query: 183 DGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLK 242
             +  G    V ++G+T GEKDF  +V RLK EN+D VY+GGYH E G + RQ    G+K
Sbjct: 182 AAINAGGITEVVYEGLTPGEKDFGAIVTRLKAENVDVVYFGGYHAEGGLLARQMHDQGVK 241

Query: 243 TQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWT 302
            Q +G +G++N     I GE+A G + T   +  + PA  P+++A+KA K  P+ AF   
Sbjct: 242 AQLLGGDGLSNTEFWAIGGEAASGTVYTNASDATRNPAAAPVIEALKA-KNIPAEAFTLN 300

Query: 303 TYAALQSLQAGLNQ---SDDPAEIAKYLKA-NSVDTVMGPLTWDEKGDLKGFEFGVFDW 357
            YAA+Q L+AG+ +   ++D   +A  +K+  ++DTV+G LT+ E GDL    F ++ W
Sbjct: 301 AYAAVQVLKAGIEKAGSTEDATAVATAIKSGEAIDTVIGKLTYGESGDLTSPSFSLYKW 359


Lambda     K      H
   0.314    0.133    0.380 

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: 412
Number of extensions: 20
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: 367
Length of database: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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