GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Sinorhizobium meliloti 1021

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate SMc02031 SMc02031 permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__Smeli:SMc02031
          Length = 349

 Score =  236 bits (603), Expect = 5e-67
 Identities = 144/347 (41%), Positives = 201/347 (57%), Gaps = 23/347 (6%)

Query: 10  ASTGAPLPAGTLGRLTTQERLRAL----GMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQ 65
           A     +PAG  G   T  +L+A+    G L  LVLL    +  T NF    NLS +A+Q
Sbjct: 5   AEKNPDIPAGGAGARKT--KLKAVVFQAGPLIALVLLMAYLAFATSNFLTLDNLSNVARQ 62

Query: 66  ASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMP------QLGMLSVPAALL 119
           ++   +LA G TFVILTGGIDLSV +I ++SA +  ++   P        G +  P A+L
Sbjct: 63  SAFVAILAVGQTFVILTGGIDLSVAAIAALSASITAVLLTQPLVLFGIDFGFVPPPVAIL 122

Query: 120 CGLLFGI----VNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIG------ 169
            G+L G+    +NG L++  K+P FI TLGT+TA RG A LV +   + + + G      
Sbjct: 123 IGILIGMAAGALNGWLISKFKIPDFIATLGTMTAFRGAALLVTDGLPVPSFNAGRQLPES 182

Query: 170 FAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVL 229
             ++G G++ GVP   +IA    A  W+VLR T LG  IYAVGGN  AA  SGI +    
Sbjct: 183 LIWVGGGQLFGVPVSALIALLCAAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTK 242

Query: 230 LFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTL 289
           +  YA+SGLLA + G++   RL +AN L +    EL +IA+V++GGT+  GG G + G++
Sbjct: 243 IMTYAISGLLAAIAGIILVGRLNSANAL-MADGEELRSIASVVIGGTNLFGGEGGVWGSI 301

Query: 290 VGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRKGSAR 336
           +GA II VL NGL LL VS  WQ I +G+VI+  V  D +RR+   R
Sbjct: 302 IGAAIIGVLGNGLNLLDVSPFWQRIAQGVVIVVVVIFDQWRRRSMTR 348


Lambda     K      H
   0.325    0.141    0.409 

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: 377
Number of extensions: 27
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: 337
Length of database: 349
Length adjustment: 29
Effective length of query: 308
Effective length of database: 320
Effective search space:    98560
Effective search space used:    98560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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:

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