GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Marinobacter adhaerens HP15

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 GFF3307 HP15_3249 TRAP-type mannitol/chloroaromatic compound transport system, large permease component

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__Marino:GFF3307
          Length = 431

 Score =  451 bits (1159), Expect = e-131
 Identities = 221/427 (51%), Positives = 315/427 (73%), Gaps = 6/427 (1%)

Query: 8   LGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYT 67
           +G +MF  ALV+L  G+PVAF+ GGVA+ FG+   G+ +F       MP RI  +M N  
Sbjct: 2   IGMIMFGVALVMLMLGFPVAFTFGGVALFFGIFAEGMDLF-----AFMPYRIMSVMQNTV 56

Query: 68  LLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATV 127
           L+A+P FIFMG +L+++ +AE+LL +MG L G L GGLA++ +LVGALLAA+TGVV A+V
Sbjct: 57  LMAVPLFIFMGVVLQRTRLAEQLLTSMGRLFGGLPGGLAISTILVGALLAASTGVVGASV 116

Query: 128 VAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSV 187
           VAMGLISLP+ML + Y+K LATG I ASGTLGQI+PPS++L++LGD LG+ VGDLF  +V
Sbjct: 117 VAMGLISLPVMLAHKYDKRLATGTICASGTLGQIVPPSIILIILGDVLGLPVGDLFKAAV 176

Query: 188 IPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLG 247
            PG+++   + +++L++  ++P+ APA+P +      K +   ++ + IPPL LI++VLG
Sbjct: 177 WPGVVLVGLYIIYILVLTRLKPETAPAMPDEPGVSRKKEVFNALLAI-IPPLALIVVVLG 235

Query: 248 SIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFS 307
           SIF G ATPTE+ A+G  GA+ LA    QF+ + +      T+++T+MV  ILIG+TAFS
Sbjct: 236 SIFTGIATPTESSALGGVGAVVLAIIYRQFSFKMVWDASKDTVKVTAMVFAILIGATAFS 295

Query: 308 LVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQK 367
           +VF    GD  + + L  LPG K GF+ ++M  + +LGFFIDF EI+FI++P+  PVA+ 
Sbjct: 296 MVFSYTGGDYLLEEWLLQLPGEKWGFIILAMVVILVLGFFIDFVEISFIIVPILAPVAEA 355

Query: 368 LGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVL 427
           +GI+++W+ +++  NLQTSFLTPPFGF+LFYL+GVAPP V T+DIY+GV+PFIL+Q+ VL
Sbjct: 356 MGINMLWFAILIAMNLQTSFLTPPFGFSLFYLKGVAPPGVRTTDIYKGVLPFILIQMFVL 415

Query: 428 LLIIIFP 434
            LI+IFP
Sbjct: 416 ALIVIFP 422


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: 611
Number of extensions: 34
Number of successful extensions: 3
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: 431
Length adjustment: 32
Effective length of query: 413
Effective length of database: 399
Effective search space:   164787
Effective search space used:   164787
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