GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Acidovorax sp. GW101-3H11

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:B2T9V8
         (351 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  125 bits (314), Expect = 4e-33
 Identities = 103/338 (30%), Positives = 161/338 (47%), Gaps = 13/338 (3%)

Query: 10  FGAAQAGAQSQLALPASRGKRA---RSELARLRELALLPALALLIVIGAFISPSFLTKAN 66
           F   +  A +  A PA+    A   RS+L     L LL  LA ++ + + +S  F +   
Sbjct: 558 FSCDRMNAPTAPAAPAATPSSASVWRSQLGTY--LGLLAVLAGMVALFSSLSEYFWSAET 615

Query: 67  LISVLGASAALALVVLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPA 126
            I++     ALA++ +  + +++    DLS+ S + +A A  A     AA   +G   PA
Sbjct: 616 FITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSA-----AAILQWGWTVPA 670

Query: 127 AAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSF 186
           AA L   +  G V G I G + V  RL +FIV+L ML  +RG     T   T + +  + 
Sbjct: 671 AAALA--LATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQY-VGDAI 727

Query: 187 FALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITW 246
             L+     G+  +  LA     +A  +L     GR +  IG N EA R AG+    I  
Sbjct: 728 SWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRV 787

Query: 247 GVFVLGSILASVGGLIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTG 306
            VF +  +LA + GL+ +  + A + N G GM   V AA VIGG SL GG+G++     G
Sbjct: 788 IVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFG 847

Query: 307 VLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMVARL 344
           VL++ V++  L          + I G +I+ +++V  L
Sbjct: 848 VLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTL 885


Lambda     K      H
   0.326    0.140    0.397 

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: 520
Number of extensions: 25
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: 351
Length of database: 892
Length adjustment: 36
Effective length of query: 315
Effective length of database: 856
Effective search space:   269640
Effective search space used:   269640
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 (21.6 bits)
S2: 53 (25.0 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