GapMind for catabolism of small carbon sources

 

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

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  200 bits (508), Expect = 1e-55
 Identities = 136/332 (40%), Positives = 191/332 (57%), Gaps = 15/332 (4%)

Query: 6   TRPAASTGAPLPAGTL-GRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQ 64
           T PAA    P  A     +L T      LG+L VL  +   FS L+E F   +    IA 
Sbjct: 567 TAPAAPAATPSSASVWRSQLGTY-----LGLLAVLAGMVALFSSLSEYFWSAETFITIAN 621

Query: 65  QASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAA----LLC 120
           +     V+A GMTFV++  GIDLSVGS+++++A  +    L  Q G  +VPAA    L  
Sbjct: 622 EIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAIL--QWGW-TVPAAAALALAT 678

Query: 121 GLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLG 180
           GL+ G + GA+    +LP FIV+LG L AVRG A +V +  T Y  D   +++      G
Sbjct: 679 GLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQYVGD-AISWLSAPFFGG 737

Query: 181 VPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLA 240
           + +  ++A  +V V+  VL RTV G  +  +G N EA RL+G+    + + V+A++GLLA
Sbjct: 738 ISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLA 797

Query: 241 GLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSN 300
           GL G+M SARL AA+    G   EL  IAAV++GGTS +GG GS+V T  G LIIAVL  
Sbjct: 798 GLAGLMQSARLEAADP-NAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVLEA 856

Query: 301 GLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332
           GL  +G S+  + II G VI+ AV +D+ R++
Sbjct: 857 GLAQVGASEPSKRIITGFVIVAAVIVDTLRQR 888


Lambda     K      H
   0.325    0.141    0.409 

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: 672
Number of extensions: 32
Number of successful extensions: 5
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: 337
Length of database: 892
Length adjustment: 35
Effective length of query: 302
Effective length of database: 857
Effective search space:   258814
Effective search space used:   258814
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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