GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Pseudomonas stutzeri RCH2

Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate GFF3943 Psest_4013 TRAP transporter, DctM subunit

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__psRCH2:GFF3943
          Length = 458

 Score =  456 bits (1173), Expect = e-133
 Identities = 237/453 (52%), Positives = 317/453 (69%), Gaps = 20/453 (4%)

Query: 6   EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65
           E++  ++F      L SGYPVAF+LGG+A+LF  +G+  G FD  +L A+P RIFGIM N
Sbjct: 3   EFMAILLFISICFALMSGYPVAFTLGGMALLFAGVGVVTGSFDVGYLHALPNRIFGIMNN 62

Query: 66  YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125
            T+LA+P F+FMG MLEKS +AE LLE+M  L G +RGGLA++V +VGALLAA+TG+V A
Sbjct: 63  QTMLAVPLFVFMGVMLEKSRVAEDLLESMSRLFGTMRGGLAISVCVVGALLAASTGIVGA 122

Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLG--------- 176
           TVV MGL++LP MLR GY+  +ATG +AA+GTLGQIIPPS++LV+LGD +          
Sbjct: 123 TVVTMGLLALPTMLRRGYDPAIATGTLAATGTLGQIIPPSIILVLLGDVMSSAFQQAQLK 182

Query: 177 --------ISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALG 228
                   +SVGDLF+G++IPGL++   + L+++ VA  +P   PALP +  E+G    G
Sbjct: 183 MGIFSPKTVSVGDLFVGALIPGLLLVGMYILYLIAVAIFQPKKLPALPQE--ELGPIEWG 240

Query: 229 KRVIQVMIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDT 288
           K +I  ++PPL LI  VLGSI  G+ATPTEA A+G  GA  L+ A GQ     L+QV   
Sbjct: 241 K-LIGSLLPPLALITAVLGSILAGYATPTEAAAIGALGATLLSIAKGQLNFTQLKQVAFG 299

Query: 289 TLRITSMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFI 348
           T  ITSMV  ILIG++ FSLVFRG  G+  + D L +LPGG +G   V M  +FLLGF +
Sbjct: 300 TTEITSMVFLILIGASLFSLVFRGFGGEVLIEDALHSLPGGVLGAFLVVMLVIFLLGFIL 359

Query: 349 DFFEIAFIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVT 408
           DF EI F+V+P+  P+   +G+D VW GV+   NLQTSFLTPPFGF+LFYLRGV P  V 
Sbjct: 360 DFIEIIFVVVPIVGPILLAMGLDPVWLGVMFAINLQTSFLTPPFGFSLFYLRGVTPRSVP 419

Query: 409 TSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLP 441
           TS +Y+GV+PFI +Q+ +L++  ++PGIV++LP
Sbjct: 420 TSVMYKGVLPFIAIQIGMLVVAYMWPGIVTWLP 452



 Score = 27.3 bits (59), Expect = 0.001
 Identities = 39/171 (22%), Positives = 71/171 (41%), Gaps = 20/171 (11%)

Query: 53  TAMPQRIFGIMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLV 112
           T +   +F I+   +L ++ +  F G +L    I + L    G +LG       L V+LV
Sbjct: 301 TEITSMVFLILIGASLFSLVFRGFGGEVL----IEDALHSLPGGVLGAF-----LVVMLV 351

Query: 113 GALLAATTGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLG 172
             LL      +    V + ++  PI+L  G +      + A +     + PP       G
Sbjct: 352 IFLLGFILDFIEIIFVVVPIVG-PILLAMGLDPVWLGVMFAINLQTSFLTPP------FG 404

Query: 173 DQL----GISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQV 219
             L    G++   +    +  G++   A  + +L+VA++ P +   LP QV
Sbjct: 405 FSLFYLRGVTPRSVPTSVMYKGVLPFIAIQIGMLVVAYMWPGIVTWLPEQV 455


Lambda     K      H
   0.331    0.149    0.437 

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: 647
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 445
Length of database: 458
Length adjustment: 33
Effective length of query: 412
Effective length of database: 425
Effective search space:   175100
Effective search space used:   175100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 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