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 GFF1039 Psest_1072 TRAP transporter, DctM subunit

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__psRCH2:GFF1039
          Length = 456

 Score =  383 bits (984), Expect = e-111
 Identities = 205/442 (46%), Positives = 294/442 (66%), Gaps = 13/442 (2%)

Query: 12  MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGV-FDPIF-------LTAMPQRIFGIM 63
           MFA  + LL  G+PVA+SL G+ +LF +LG  L   FD          +  +  RI+GI+
Sbjct: 11  MFASFMGLLLLGFPVAWSLAGIGLLFAVLGYVLVEHFDANLWFTWDGTIGVLDARIYGIV 70

Query: 64  ANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVV 123
           AN  ++A+P FIFMG ML++SGIAERL+ ++  +LG LRGG A+ VV+VG LLAA+TG+V
Sbjct: 71  ANELMVALPLFIFMGIMLDRSGIAERLMHSLVRVLGPLRGGYAVTVVVVGILLAASTGIV 130

Query: 124 AATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGIS---VG 180
            A+V  +G++S+  ML+  YNK LA G   + GTLG +IPPS++LV++ D+LG S   VG
Sbjct: 131 GASVALLGMLSIGPMLQANYNKSLAVGTACSVGTLGILIPPSIMLVLMADRLGTSEASVG 190

Query: 181 DLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLI 240
            LF+G++IPG+M+A  + L+++IVA+++ D APA P    ++  +AL   V   ++PPL 
Sbjct: 191 KLFMGALIPGMMLALMYILYIVIVAWLKKDFAPA-PVNRPKLDARAL-LDVFWAVVPPLA 248

Query: 241 LILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFIL 300
           LI  VLGSIFFG AT TEA AVG  GA+ +AAA+ +  L  L+     T R  + +  I 
Sbjct: 249 LIFAVLGSIFFGIATTTEASAVGAFGALLMAAASRRLNLPVLKDALYQTSRTAAFIFGIF 308

Query: 301 IGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPL 360
           IG+T F+ V RGL GD  +   L  LP G+ G L   +   FLLGFF+D+ EI  I++PL
Sbjct: 309 IGATVFAAVLRGLGGDDVIRAALTGLPFGQTGVLLTVLAITFLLGFFLDWVEITLIILPL 368

Query: 361 FVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFI 420
             PV   +G+D +W+ ++    LQTSFLTPP GFALFY++GV PP +TT D+Y GV+P+I
Sbjct: 369 VAPVLFSMGVDPLWFAILFALCLQTSFLTPPVGFALFYIKGVCPPGITTRDVYLGVLPYI 428

Query: 421 LLQLLVLLLIIIFPGIVSFLPS 442
           ++QL+ L L+  F  + ++LP+
Sbjct: 429 VIQLIGLALVFYFAPLATWLPN 450


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: 569
Number of extensions: 26
Number of successful extensions: 5
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: 445
Length of database: 456
Length adjustment: 33
Effective length of query: 412
Effective length of database: 423
Effective search space:   174276
Effective search space used:   174276
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