GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Azospirillum brasilense Sp245

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate AZOBR_RS31230 AZOBR_RS31230 gluconolactonase

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__azobra:AZOBR_RS31230
          Length = 299

 Score =  158 bits (399), Expect = 2e-43
 Identities = 96/298 (32%), Positives = 148/298 (49%), Gaps = 12/298 (4%)

Query: 5   KIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVE-APIGSVAL 63
           ++ CV      +GE P+W  ++G + FVDI G ++ R           ++E A    V  
Sbjct: 4   EVRCVWPARALLGEGPLWSPEQGAVFFVDIHGSRILRHGLDDGSQADWALEDAACWLVEC 63

Query: 64  RKSGGYVLAM-GNTFSALNWEDQSVT---TLARVDEDKPNNRFNDGKVDPEGRFLAGTMS 119
               G++  +       L  E         LAR+D D+P NR ND K D +GR   G+M 
Sbjct: 64  ADGDGFIAGLRSRRVVRLRLEPGRAVIAGELARIDPDRPGNRLNDAKADAQGRLWIGSMD 123

Query: 120 QEIRPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALD 179
                   E   G+   L PD S+ +  +   ++NG   S D +TLY+ DS +  + A D
Sbjct: 124 DG-----EETPSGAFHRLDPDGSITRMDEGYTVANGPALSPDGRTLYHTDSAARTIHAFD 178

Query: 180 YDMKTGKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVK 239
            D   G+ S +R   +  + +G PDGM  DAEG LWVA ++GGRV R  P+ G   + + 
Sbjct: 179 LD-GAGRLSGKRAHIRFAEADGYPDGMTCDAEGGLWVAHWDGGRVSRFRPD-GTLDRAIA 236

Query: 240 LPIDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAF 297
           LP+ + TSC F GP    ++VT+A  G+  D +  +P +G +++    GV+G+ P  F
Sbjct: 237 LPVSRVTSCVFAGPALDRLFVTTAAHGIGRDGRPDEPLAGALFECDPGGVRGLPPGRF 294


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: 338
Number of extensions: 25
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 299
Length of database: 299
Length adjustment: 27
Effective length of query: 272
Effective length of database: 272
Effective search space:    73984
Effective search space used:    73984
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