GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Herbaspirillum seropedicae SmR1

Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease

Query= uniprot:A0KWY6
         (405 letters)



>FitnessBrowser__HerbieS:HSERO_RS03645
          Length = 339

 Score =  165 bits (417), Expect = 2e-45
 Identities = 103/271 (38%), Positives = 162/271 (59%), Gaps = 9/271 (3%)

Query: 98  IDILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLLL--VPDISLVTVIAA 155
           ++IL + A   +L+ GM+ VI T GIDLSVG+V+A++  +   + L   P  ++   I +
Sbjct: 62  MNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFS 121

Query: 156 GLIVGLLAGCINGGLVSFLGIQPIVATLLLMVAGRGVAQLINQGQ-IITFQHPGFAAIGV 214
           GL++G+    +NG +V+ L I   V TL  M A RG A L+  G  ++    P F  IG 
Sbjct: 122 GLVMGM----VNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGN 177

Query: 215 GQFLGLPMPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGI 274
           G FL +P  +W+ + ++  S ++LRKT LG+ I A+G N +A+R  GI    + LF Y I
Sbjct: 178 GDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSI 237

Query: 275 AGLCAALAGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALII 334
           +GL + LAG +S + + G++  N G   ELDA+ AVV+GG +L GG  S+  +VVGALII
Sbjct: 238 SGLFSGLAGAMSASRLYGAN-GNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALII 296

Query: 335 QTLATTIIVSGLPAKFNLLIK-AIVILTVLL 364
             +   + + GL + +  + K A+++L V+L
Sbjct: 297 GVMNNGLTILGLSSFWQYVAKGAVIVLAVIL 327


Lambda     K      H
   0.323    0.136    0.379 

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: 300
Number of extensions: 18
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: 405
Length of database: 339
Length adjustment: 30
Effective length of query: 375
Effective length of database: 309
Effective search space:   115875
Effective search space used:   115875
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 (22.0 bits)
S2: 49 (23.5 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