GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaS in Pseudomonas simiae WCS417

Align RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate GFF3595 PS417_18405 LacI family transcriptional regulator

Query= TCDB::Q7BSH5
         (331 letters)



>FitnessBrowser__WCS417:GFF3595
          Length = 318

 Score = 97.4 bits (241), Expect = 4e-25
 Identities = 91/306 (29%), Positives = 135/306 (44%), Gaps = 29/306 (9%)

Query: 10  GVALAVAMMAGTASAKDI-----------KIGLVVKSLGNGFFDAANKGAQEAAKE-LGG 57
           G  LAVA++A  ++A  +           K+GLV+KSL N FF     GA+   KE    
Sbjct: 7   GRLLAVAVLAAASAALPLSSAFADDAAKPKVGLVMKSLANEFFVTMQDGAKTYQKEHAAD 66

Query: 58  VEVIYTG-PTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWD 116
            ++I  G    T    QI+++N +I   V+AI ++  D  ALV  LKKA+  GIKV++ D
Sbjct: 67  FDMITNGIKNETDTSAQIDIVNQMILAKVNAIVIAPADSKALVTVLKKASDAGIKVVNID 126

Query: 117 SGVAPE---GRILQL------NPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQ 167
           + + P+    + L +      N   ++L+G     LAK    G K        TTT+  Q
Sbjct: 127 NRLDPDVLKSKNLDIPFVGPDNRKGSKLVGDY---LAKQLASGDKVGIIEGVPTTTNAQQ 183

Query: 168 NIWIDQMKKQLKDFPGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAA 227
                   K   D  G+ +V+T  G+   D+  + A  +L   P++K ++A      L A
Sbjct: 184 R---TAGYKDAMDAAGMKIVSTQSGNWEIDQGQKVASAMLSEYPDLKALLAGNDNMALGA 240

Query: 228 SKVVEDKGLVGKVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGE- 286
              V   G  GKV V G      +   ++ G     A            Q A +LVKGE 
Sbjct: 241 VSAVRAAGKAGKVLVVGYDNIEAIKPMLQDGRVLATADQAAAQQAVFGIQNALKLVKGEK 300

Query: 287 TDGKPG 292
            D K G
Sbjct: 301 VDSKDG 306


Lambda     K      H
   0.313    0.131    0.365 

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: 252
Number of extensions: 17
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: 318
Length adjustment: 28
Effective length of query: 303
Effective length of database: 290
Effective search space:    87870
Effective search space used:    87870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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