GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Pseudomonas fluorescens GW456-L13

Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (characterized)
to candidate PfGW456L13_3930 Gluconate dehydratase (EC 4.2.1.39)

Query= SwissProt::Q12DF1
         (395 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3930
          Length = 394

 Score =  696 bits (1797), Expect = 0.0
 Identities = 326/392 (83%), Positives = 355/392 (90%)

Query: 4   MPTIKHVRAFTVRGGGADYHDQGSGHWIDDHISTPMGRYPEYRQSRQSFGINVLGTLVVE 63
           +PTIKHVRAFT+RGGGADYHDQ  GHWIDDHI+TPM +YPEYRQSR++FGINVLGTLVVE
Sbjct: 3   IPTIKHVRAFTLRGGGADYHDQADGHWIDDHIATPMSKYPEYRQSRRTFGINVLGTLVVE 62

Query: 64  IEASDGTVGFSVTTGGELGCWIVEKHLARFIEGAKVTDIEKIWDQMFNATLYYGRKGIVL 123
           IEASDGTVGF+VTTGGE   +IVEKHLARF+EG +VTDIEKIWDQM+ +TLYYGRKGIV+
Sbjct: 63  IEASDGTVGFAVTTGGEPAAYIVEKHLARFLEGVRVTDIEKIWDQMYQSTLYYGRKGIVI 122

Query: 124 NTISGVDLALWDLLAKVRKEPVHALLGGPVRDELTFYATGARPDLAKKMGFIGGKLPLHH 183
           NTISGVDLALWDLL K+R+EPVH LLGG VRDEL FYATGARPDLA+KMGFIGGK+PLHH
Sbjct: 123 NTISGVDLALWDLLGKIRQEPVHQLLGGAVRDELQFYATGARPDLAQKMGFIGGKMPLHH 182

Query: 184 GPAEREEGLKKNLELLGEMRQRVGDDFWLMYDCWMSLDVEYATRLANAASEYKLKWIEEA 243
           GPAE EEGL+KNLE L  MR+RVG DFWLM DCWMSLD+ YAT+LA  A EY LKWIEEA
Sbjct: 183 GPAEGEEGLRKNLEELATMRERVGPDFWLMLDCWMSLDLNYATKLAVGAHEYGLKWIEEA 242

Query: 244 LPPDDYWGYAELRRNVPRGMLVTTGEHEATRWGFRMLLEMECCDILQPDVGWCGGITELL 303
           LPPDDYWGYA LR NVP+GMLVTTGEHEATRWGFRMLLEM CCDI+QPDVGWCGGITEL+
Sbjct: 243 LPPDDYWGYAALRNNVPKGMLVTTGEHEATRWGFRMLLEMGCCDIIQPDVGWCGGITELV 302

Query: 304 KISALADAHGKLVVPHGSSVYSYHFVITRHNSPFSEFLMMAPKADEVVPMFNPMLLDEPV 363
           KISALADAH  LV+PHGSSVYSYHFV TRHNSPF+EFLMMAPKADEVVPMF+P LL EPV
Sbjct: 303 KISALADAHNALVIPHGSSVYSYHFVATRHNSPFAEFLMMAPKADEVVPMFHPQLLGEPV 362

Query: 364 PVNGRMKASALDAPGFGVRLNPECALQRPFPR 395
           PVNGRM+ SALD PGFGV LNPEC L RP+ R
Sbjct: 363 PVNGRMRLSALDQPGFGVTLNPECQLHRPYNR 394


Lambda     K      H
   0.321    0.140    0.444 

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: 625
Number of extensions: 16
Number of successful extensions: 1
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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: 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