GapMind for catabolism of small carbon sources

 

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

Align L-arabinonolactonase (characterized, see rationale)
to candidate H281DRAFT_05978 H281DRAFT_05978 Sugar lactone lactonase YvrE

Query= uniprot:A0A1I2AUG6
         (300 letters)



>FitnessBrowser__Burk376:H281DRAFT_05978
          Length = 303

 Score =  192 bits (487), Expect = 1e-53
 Identities = 120/291 (41%), Positives = 156/291 (53%), Gaps = 10/291 (3%)

Query: 5   VVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALCEAD 64
           VV    + LGE I+W E+ Q L+W D    ++ R   + GA +SW M E +G + L  A 
Sbjct: 19  VVDSTPDVLGESIIWDEKTQLLWWVDGIGQSIHRLDISSGAKKSWPMQEEIGSIGL-RAK 77

Query: 65  GWLLLGLATRLAFFRPEDDLLLPLVSVEPDLP-TRLNDGACDRQGRFVFGTLHEPAAGET 123
           G L++G+ +   FF PE   L  +   + + P  R NDG CDR GR+  GT+   AA  T
Sbjct: 78  GGLIVGMRSGFYFFSPETGELTEVARPDAERPKNRFNDGKCDRHGRYWSGTVE--AAAYT 135

Query: 124 RQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDRCG- 182
             P G  +RL+ DL   +L + GI   N ++FSPD R MY  DS S  I   DY    G 
Sbjct: 136 --PRGRLFRLDPDLK-PKLIMEGITCINGLSFSPDNRLMYMTDSFSCQIDVFDYDSVDGA 192

Query: 183 --EPRVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQPTR 240
               R FA V   RG  DGS VDA GC W+A      V RY P GR+D ++ +P  + + 
Sbjct: 193 IYNRRKFAEVPLGRGICDGSTVDADGCFWSANMDGWCVTRYDPRGRIDMVINLPVRRVSS 252

Query: 241 PAFGDSPLDTLYITSARDGLSSAALATQPLAGALFAADAGASGLPEPRFRG 291
             FG   LDTL+IT+AR  +S   LA QPLAG + A   G  GLPEP F G
Sbjct: 253 LCFGGPDLDTLFITTARRRMSEKELAQQPLAGNVLAVRPGVKGLPEPEFLG 303


Lambda     K      H
   0.321    0.139    0.451 

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: 339
Number of extensions: 22
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: 300
Length of database: 303
Length adjustment: 27
Effective length of query: 273
Effective length of database: 276
Effective search space:    75348
Effective search space used:    75348
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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