GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Sinorhizobium meliloti 1021

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate SMc04142 SMc04142 hypothetical protein

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__Smeli:SMc04142
          Length = 294

 Score =  139 bits (351), Expect = 6e-38
 Identities = 98/295 (33%), Positives = 142/295 (48%), Gaps = 11/295 (3%)

Query: 4   IKIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVAL 63
           +  EC++     + ESPV++E+   L FVDI    + R D S       ++E    S  L
Sbjct: 5   LTFECLLDSRCDVAESPVFDERRNCLFFVDIGRSALHRVDLSGAGHVEWTIEGGACSTGL 64

Query: 64  RKSGGYVLAMGNTFSALNWEDQSVTT-LARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEI 122
            +SG  VLA  +     + +  +VT  +A ++ D  + R NDGKV P+G F  GTM    
Sbjct: 65  ARSGRLVLAQRDRVVLFDPDAGAVTREIAAIEPDIADTRLNDGKVGPDGAFWVGTMHD-- 122

Query: 123 RPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDM 182
                 R   SL+ + P+ +V +  + V  SNGL WS D   L++ DS    +D   +D 
Sbjct: 123 --VPDRRPVASLYRVSPEGAVERKVEGVVCSNGLAWSGDGSLLFHSDSRGAWIDRWQFDP 180

Query: 183 KTGKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPI 242
            TG  S RR L  L +  G PDG   DAE   W A  + G V R  PE G+ + T + P+
Sbjct: 181 ATGALSGRRRLASLDEASGRPDGAATDAEAHYWSAGVSAGIVNRFSPE-GRLVGTHRFPV 239

Query: 243 DKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAF 297
              T  CF GPD   + VTS    +      ++ +SGGI+ +    V G+A   F
Sbjct: 240 PAPTMPCFAGPDLKTLLVTS----LRPAGIGKENRSGGIF-VARSPVAGVAVHRF 289


Lambda     K      H
   0.316    0.135    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: 292
Number of extensions: 17
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: 299
Length of database: 294
Length adjustment: 26
Effective length of query: 273
Effective length of database: 268
Effective search space:    73164
Effective search space used:    73164
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: 41 (21.6 bits)
S2: 48 (23.1 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