GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Pedobacter sp. GW460-11-11-14-LB5

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein

Query= TCDB::P15729
         (468 letters)



>FitnessBrowser__Pedo557:CA265_RS01275
          Length = 462

 Score =  268 bits (684), Expect = 4e-76
 Identities = 164/462 (35%), Positives = 250/462 (54%), Gaps = 26/462 (5%)

Query: 16  FVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAFGAG 75
           F+ LI+ +AALGGFLFGFD AV++G +  L+  +   S   GL VS ALLG  +G   +G
Sbjct: 9   FIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSG 68

Query: 76  PIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEV 135
            ++D+ GR K + LAA+LF +S++G          IF+RVL G+GVG AS ++P YI+EV
Sbjct: 69  YLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEV 128

Query: 136 SPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMA-----GGSAQNPWLFGAAAWRWMFW 190
           +P+  RGRL    QLAI  GI  A +SN F+   A      G     WLF    WR MF 
Sbjct: 129 APSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFI 188

Query: 191 TELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVP----SRIEEIQATVS 246
             ++PA  + +   ++PESPR+LV  G+ E+A   L K+ G +        I+E+ +  S
Sbjct: 189 VGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKINGAETGRLELDSIKEMASQKS 248

Query: 247 LDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLI 306
             +K      LS+   L  I      L+AL QF GIN + +Y   + +S G     +L  
Sbjct: 249 GGYKELMRLPLSKLLALATI------LTALSQFSGINGVIFYGPTILKSAGIVTSDALFY 302

Query: 307 TVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTG 366
            VI G  N+L T +AI+ VD +GR+PL ++GS+              GA  + G   L  
Sbjct: 303 QVILGSANVLFTFIAISKVDTWGRRPLYIIGSL-----------CAAGALALTGFCFLMD 351

Query: 367 AAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTF 426
             G   L +  L++  F FS GP+ +V+  E+F   IR  ALS+     W+++++++  F
Sbjct: 352 ITGWFMLFSIILFLLFFAFSLGPLKFVISTEIFPTHIRGTALSMCIMTMWVSDWVVNMLF 411

Query: 427 PPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
           P + D +G+   + +++    +S  +    + ETKGK+LE++
Sbjct: 412 PIMRDGLGIATTFFIFSFFCILSFLYAKKKLFETKGKSLEEI 453


Lambda     K      H
   0.325    0.140    0.430 

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: 534
Number of extensions: 28
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: 468
Length of database: 462
Length adjustment: 33
Effective length of query: 435
Effective length of database: 429
Effective search space:   186615
Effective search space used:   186615
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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