GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Dechlorosoma suillum PS

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= uniprot:Q31RN9
         (396 letters)



>FitnessBrowser__PS:Dsui_0636
          Length = 245

 Score =  103 bits (258), Expect = 4e-27
 Identities = 73/232 (31%), Positives = 127/232 (54%), Gaps = 25/232 (10%)

Query: 180 LRPVSSND-------WSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLS---VT 229
           L PV S +       ++GL  T+A +L + V +L +G ++ + R  ++P  RWLS     
Sbjct: 11  LTPVPSGETTYLGWLFTGLQWTVALSLSAWVIALVVGSIVGVLR--TVPN-RWLSGFAAV 67

Query: 230 YIELFRGLPLVTILFFGQVMVPLML---------DSEWRIDRILRAIVGLTIFLSAYLAE 280
           Y+E FR +PL+  LF    ++P +L          S+  + + L A++ L +F +A +AE
Sbjct: 68  YVECFRNVPLLVQLFSWYFVLPELLPPALGNAYKQSDPLLQQFLAAMLCLGLFTAARVAE 127

Query: 281 TVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSI 340
            VR G++++P+GQ  A  A+G  L Q YR ++LP A RI +P +   FLN+ +++ + + 
Sbjct: 128 QVRAGIESLPRGQRNAGLAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKNSAVATT 187

Query: 341 VGLLELLGISRSILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392
           +GL+EL   SR       Y  +  E ++ + +LY      +  L RRLE+++
Sbjct: 188 IGLIEL---SRQAQQLVDYTAQPYEAFIAVTLLYVCINVTVMFLMRRLEEKV 236


Lambda     K      H
   0.329    0.142    0.471 

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: 264
Number of extensions: 11
Number of successful extensions: 2
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: 396
Length of database: 245
Length adjustment: 27
Effective length of query: 369
Effective length of database: 218
Effective search space:    80442
Effective search space used:    80442
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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