GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pseudomonas simiae WCS417

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  385 bits (990), Expect = e-111
 Identities = 215/503 (42%), Positives = 322/503 (64%), Gaps = 11/503 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPD-AGEIL 72
           +L+ +GI K F G+  +  V  +VY  EI +L+GENGAGKSTL+KIL+G  + D  GEI 
Sbjct: 6   LLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIR 65

Query: 73  VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132
           + G+ +    P  A   GI+VI+QEL+LC N++VAENI+L  E  RG        +D   
Sbjct: 66  IAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWT------IDRKG 119

Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192
           M     E+L  +GA+F+P   V +L+ A+RQ+VEI +AL    +I+ MDEPT+ L+  ET
Sbjct: 120 MEAGCIEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRET 179

Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252
           +RLF +I+ L+S+G++++++SHR+ E+  +SDR+ V+RDG  IGEL +     + ++KMM
Sbjct: 180 DRLFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMM 239

Query: 253 VGREVEFF--PHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTET 310
           VGR++  F         PG + + VR++    +V++ SF++  GEVLG AGLVGAGRTE 
Sbjct: 240 VGRDLSGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTEL 299

Query: 311 MLLVFGVNQKESGDIYVNGRKVE-IKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVL 369
             L+F  + + SG + V G+ V  ++ P DAI+ G+  + EDRK QGL L M+V DNI +
Sbjct: 300 ARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINV 359

Query: 370 PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATN 429
            +    +  G VLD     + S D +K LSI+  S       LSGGNQQKV+LA+ L   
Sbjct: 360 CACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVK 419

Query: 430 ADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEI 489
             +LI DEPTRG+D+G+K+EI+R+I +LA  G  +++ISSELPEI+   DR+++M EG++
Sbjct: 420 PHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQL 479

Query: 490 TAVLDNRE-KRVTQEEIMYYASG 511
            A +     + ++QE I+  A+G
Sbjct: 480 VAEVGGASGQAISQERIIDLATG 502


Lambda     K      H
   0.319    0.138    0.381 

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: 632
Number of extensions: 37
Number of successful extensions: 8
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: 520
Length of database: 510
Length adjustment: 35
Effective length of query: 485
Effective length of database: 475
Effective search space:   230375
Effective search space used:   230375
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 (21.7 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