GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Acidovorax sp. GW101-3H11

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= SwissProt::P37772
         (331 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  137 bits (344), Expect = 1e-36
 Identities = 90/251 (35%), Positives = 135/251 (53%), Gaps = 5/251 (1%)

Query: 29  FASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVIGDFGLSPL 88
           F S      I  +   L ++AVGMTFV++  GIDLSVGSV+A      A  I  +G +  
Sbjct: 610 FWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQWGWTVP 669

Query: 89  LAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDT 148
            A  L L  G   G   G +  A ++P+FI++L  +  +RG +Y+V++        + D 
Sbjct: 670 AAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQY---VGDA 726

Query: 149 LSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQVYAIGGNATSANLMGISTRS 208
           +S L+    GG  +S   LL + +VV+   +  RT FG  V  IG N  +  L G+  R 
Sbjct: 727 ISWLSAPFFGG--ISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRP 784

Query: 209 TTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGT 268
             + ++ ++  LA LAG++ S   +A    AG G+EL  IA+VVIGGT L GG G+V+ T
Sbjct: 785 IRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNT 844

Query: 269 LFGVAIQGLIQ 279
            FGV I  +++
Sbjct: 845 AFGVLIIAVLE 855


Lambda     K      H
   0.329    0.145    0.428 

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: 617
Number of extensions: 27
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: 331
Length of database: 892
Length adjustment: 35
Effective length of query: 296
Effective length of database: 857
Effective search space:   253672
Effective search space used:   253672
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: 52 (24.6 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