GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Rhodobacter viridis JA737

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_003217355.1:WP_110804905.1
          Length = 262

 Score =  113 bits (282), Expect = 4e-30
 Identities = 72/226 (31%), Positives = 119/226 (52%), Gaps = 13/226 (5%)

Query: 6   ADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLT 65
           A +  +L     +T+ +T+++  GA++ G +L    +S   I R L+  Y   +R  P+ 
Sbjct: 34  AKIFATLSKGIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPII 93

Query: 66  LVVLFCSFGL-------YQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRS 118
           +++L+ +F L       +  LGL  A       L       AVL  IL  + F+AE  R+
Sbjct: 94  VMLLYVAFALVPAVVAGWNALGLPEASVRDFPLLAR-----AVLALILAYAAFLAEVFRA 148

Query: 119 GINTVHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVG 178
           G+ +V  GQ EAA++LGL     FR IIFPQA R  + PLGN  +A+ K++++ SV+GV 
Sbjct: 149 GLLSVERGQIEAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVA 208

Query: 179 EASLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224
           + + L K T   +    F  + + A+ ++ +T+ + L L KL   L
Sbjct: 209 DITQLGKVTAAGNFR-YFETYNVVALIYLAMTVTLSLALRKLEAHL 253


Lambda     K      H
   0.327    0.139    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: 146
Number of extensions: 9
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: 228
Length of database: 262
Length adjustment: 24
Effective length of query: 204
Effective length of database: 238
Effective search space:    48552
Effective search space used:    48552
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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