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 SMa0717 SMa0717 hypothetical protein

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__Smeli:SMa0717
          Length = 569

 Score =  170 bits (431), Expect = 6e-47
 Identities = 98/294 (33%), Positives = 158/294 (53%), Gaps = 8/294 (2%)

Query: 6   IECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRK 65
           ++CV+    ++GE+PVW E+E  L +VDI    V R+DP T K +S +V   + +V   +
Sbjct: 283 VQCVLPWGAQLGEAPVWVEREKRLYWVDILHPAVHRFDPVTGKNESCNVAKLVSAVLPTR 342

Query: 66  SGGYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPA 125
           + G ++A  +     +++       A  +   P NR ND KVDP GR   G+M  +    
Sbjct: 343 NEGLIVASQDGVEHFDFDRGDFNPFAEPEPGLPENRLNDAKVDPSGRLWVGSMRLD---- 398

Query: 126 VVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTG 185
            V R  GSL+ L     V +      ++NGL WS D  T Y++D++   + A D+D + G
Sbjct: 399 -VSRPTGSLYRLTSAGEVTRAGSGFTVANGLAWSPDSSTFYFVDTVPGIIYAYDFDAREG 457

Query: 186 KSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKT 245
             +NRR    + + EG PDG+ +DA+G +W A ++G RV R  P+ G+  + V+LP+ + 
Sbjct: 458 SIANRRVFVTVPEAEGRPDGLAVDADGGVWCAIWDGWRVNRYRPD-GRLDRAVELPVPRP 516

Query: 246 TSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299
           TS  FGG + + +++TSA   +        P SGGI+     G +G+ PT+  G
Sbjct: 517 TSVAFGGDELATLFITSARTRLPASTLTEAPLSGGIFACNP-GARGL-PTSLFG 568


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: 484
Number of extensions: 30
Number of successful extensions: 3
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: 569
Length adjustment: 31
Effective length of query: 268
Effective length of database: 538
Effective search space:   144184
Effective search space used:   144184
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: 50 (23.9 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