GapMind for catabolism of small carbon sources

 

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

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein

Query= SwissProt::P96710
         (464 letters)



>FitnessBrowser__Pedo557:CA265_RS01275
          Length = 462

 Score =  328 bits (840), Expect = 3e-94
 Identities = 181/451 (40%), Positives = 257/451 (56%), Gaps = 12/451 (2%)

Query: 22  FVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISG 81
           F+ LI+  A LGG L+G+D AV+SG I  LK  Y LS   EGL +S  ++G +VGV  SG
Sbjct: 9   FIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSG 68

Query: 82  FLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEA 141
           +LSD+ GRRK+L  AA+LF +SA+  A S     LI  R++ G+G+G+ S++S  YI+E 
Sbjct: 69  YLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEV 128

Query: 142 APPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTG----------WRWMLA 191
           AP   RG L   YQL   +GI A Y  NL +QR  T   G   G          WR M  
Sbjct: 129 APSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFI 188

Query: 192 YGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQ 251
            G+VP+  F L+LL+VPESPRWL + G+  EAL  L +ING    + EL +I+  +  ++
Sbjct: 189 VGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKINGAETGRLELDSIK-EMASQK 247

Query: 252 MGSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVG 311
            G   +L +  L K L +  +L   +Q  G+N + +YGP I K  G   +       I+G
Sbjct: 248 SGGYKELMRLPLSKLLALATILTALSQFSGINGVIFYGPTILKSAGIVTSDALFYQVILG 307

Query: 312 VVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVA 371
              V+FT IA+  +D  GR+ L  IGS   A  + L G  F  ++T   M+  +IL F+ 
Sbjct: 308 SANVLFTFIAISKVDTWGRRPLYIIGSLCAAGALALTGFCFLMDITGWFMLFSIIL-FLL 366

Query: 372 AFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWI 431
            F  S+GP+ +++ +EIFP H+R  A  +  + +W ++W +    P+M D  G+A TF+I
Sbjct: 367 FFAFSLGPLKFVISTEIFPTHIRGTALSMCIMTMWVSDWVVNMLFPIMRDGLGIATTFFI 426

Query: 432 FAVINILCFLFVVTICPETKNKSLEEIEKLW 462
           F+   IL FL+      ETK KSLEEIEK W
Sbjct: 427 FSFFCILSFLYAKKKLFETKGKSLEEIEKAW 457


Lambda     K      H
   0.327    0.142    0.425 

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: 577
Number of extensions: 28
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: 464
Length of database: 462
Length adjustment: 33
Effective length of query: 431
Effective length of database: 429
Effective search space:   184899
Effective search space used:   184899
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 (21.7 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