GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Pseudomonas simiae WCS417

Align Amino-acid permease RocE (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease

Query= SwissProt::P39137
         (467 letters)



>FitnessBrowser__WCS417:GFF1065
          Length = 472

 Score =  320 bits (821), Expect = 5e-92
 Identities = 168/446 (37%), Positives = 256/446 (57%), Gaps = 4/446 (0%)

Query: 8   GNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCL 67
           G  L+R +  RH+ +++LG  IG G FLG+   I  AGP   +LSY++GG  + + M  L
Sbjct: 15  GGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRAL 73

Query: 68  GELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHID 127
           GE+AV  PV+GSF  YA  ++ P  GF  GW YW  W VTC  E  +    M  WFP   
Sbjct: 74  GEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTP 133

Query: 128 VWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQ 187
            WIW L     M  +N I  KAF E EFWF+ IKI+ I+  +I GG  +        G  
Sbjct: 134 RWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVI-GGVGIIAFGFGNDGVA 192

Query: 188 APFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVW 247
                 +   G  PNG++ +L+++  V FA+ G E+IG+ AGE+++P+KTIP +I    W
Sbjct: 193 LGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFW 252

Query: 248 RTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSG 307
           R L+F+V ++ VI  + PW + G   SPFV  FE++GI  AA I+NFV++ A LS  N G
Sbjct: 253 RILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGG 312

Query: 308 LYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLL 367
           ++++ R+LY++A  GQA     KT+  GVP  +L++++    L +L  +   E V++ + 
Sbjct: 313 IFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVT 372

Query: 368 SLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISL 427
           S+A   A   W+ I L+Q+ FR+       +   LK++  LYPV   + L    +V+  +
Sbjct: 373 SIATFGAIWTWLMILLAQLKFRKSL--SPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLM 430

Query: 428 AFDPEQRIALYCGVPFMIICYIIYHV 453
           A+ P+ RIALY G  F+++  ++++V
Sbjct: 431 AYFPDTRIALYVGPVFLVLLTVLFYV 456


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: 592
Number of extensions: 32
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.

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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