GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Paraburkholderia bryophila 376MFSha3.1

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate H281DRAFT_05978 H281DRAFT_05978 Sugar lactone lactonase YvrE

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__Burk376:H281DRAFT_05978
          Length = 303

 Score =  178 bits (452), Expect = 1e-49
 Identities = 106/294 (36%), Positives = 156/294 (53%), Gaps = 7/294 (2%)

Query: 6   IECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRK 65
           I+ V S    +GES +W+EK   L +VD  GQ + R D S+   +S  ++  IGS+ LR 
Sbjct: 17  IDVVDSTPDVLGESIIWDEKTQLLWWVDGIGQSIHRLDISSGAKKSWPMQEEIGSIGLRA 76

Query: 66  SGGYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPA 125
            GG ++ M + F   + E   +T +AR D ++P NRFNDGK D  GR+ +GT+      A
Sbjct: 77  KGGLIVGMRSGFYFFSPETGELTEVARPDAERPKNRFNDGKCDRHGRYWSGTVE-----A 131

Query: 126 VVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTG 185
                +G LF L PD       + +   NGL +S D++ +Y  DS S ++D  DYD   G
Sbjct: 132 AAYTPRGRLFRLDPDLKPKLIMEGITCINGLSFSPDNRLMYMTDSFSCQIDVFDYDSVDG 191

Query: 186 KSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKT 245
              NRR   ++    GI DG  +DA+G  W A  +G  V R DP  G+    + LP+ + 
Sbjct: 192 AIYNRRKFAEVPLGRGICDGSTVDADGCFWSANMDGWCVTRYDPR-GRIDMVINLPVRRV 250

Query: 246 TSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299
           +S CFGGPD   +++T+A   M E    +QP +G +  +   GVKG+    F G
Sbjct: 251 SSLCFGGPDLDTLFITTARRRMSEKELAQQPLAGNVLAVRP-GVKGLPEPEFLG 303


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: 316
Number of extensions: 28
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: 303
Length adjustment: 27
Effective length of query: 272
Effective length of database: 276
Effective search space:    75072
Effective search space used:    75072
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