GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Cupriavidus basilensis 4G11

Align Amino-acid permease RocE (characterized)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease

Query= SwissProt::P39137
         (467 letters)



>FitnessBrowser__Cup4G11:RR42_RS28305
          Length = 472

 Score =  308 bits (788), Expect = 3e-88
 Identities = 161/429 (37%), Positives = 252/429 (58%), Gaps = 6/429 (1%)

Query: 11  LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70
           L R +K RH+ MI++GG IG G FLG G  I  AGP G +LSY +GG  +F  M  LGEL
Sbjct: 19  LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGP-GLMLSYAIGGVAIFFIMRALGEL 77

Query: 71  AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130
            +  PVSGSF TYA +F+ P  GFA GW YW  W VT   E  +    +  WFP +  WI
Sbjct: 78  LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137

Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMF-GLIDLKGGEQAP 189
             L   A+++++N +    F E EFWF+ IK++ I+  I++G A +F G+  L  G  A 
Sbjct: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPL--GPTAS 195

Query: 190 FLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249
           F   +   G  P G   +++T+  V FA+QG ELIGV AGE+++PEK +P +    VWR 
Sbjct: 196 FSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRI 255

Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309
           L+F+V ++I++  ++PW +     SPFV VFE+IG+P AA I+N V++ A  S  NSG++
Sbjct: 256 LIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIF 315

Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSL 369
           ++ R+LY +A  GQA +A G+ + + VP  ++  + A+  + +L  +   E V++ + S+
Sbjct: 316 STGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSI 375

Query: 370 AGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAF 429
           + + +   W  I ++ + +R+      G+++ + F+ P  P    + +     V + L+ 
Sbjct: 376 SLVGSLWTWSIIMIAHLGYRKAI--AAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSL 433

Query: 430 DPEQRIALY 438
           DP  R+ALY
Sbjct: 434 DPGTRVALY 442


Lambda     K      H
   0.329    0.142    0.438 

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: 548
Number of extensions: 23
Number of successful extensions: 4
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: 467
Length of database: 472
Length adjustment: 33
Effective length of query: 434
Effective length of database: 439
Effective search space:   190526
Effective search space used:   190526
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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