GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BT0355 in Pedobacter sp. GW460-11-11-14-LB5

Align Na+/glucose cotransporter (characterized, see rationale)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter

Query= uniprot:Q8AAV7
         (564 letters)



>FitnessBrowser__Pedo557:CA265_RS04220
          Length = 550

 Score =  328 bits (840), Expect = 4e-94
 Identities = 181/573 (31%), Positives = 320/573 (55%), Gaps = 43/573 (7%)

Query: 5   DWLVIGVFFLALIGIIVWV-VRQKQND---SADYFLGGRDATWLAIGASIFASNIGSEHL 60
           D ++   + L ++ I +W   R+K+N+   S +YFL G+   W  IG ++FA+NI   HL
Sbjct: 6   DIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNISCLHL 65

Query: 61  IGLAGAGASSGMAMAHWE-IQGWMILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTIL 119
           + LA +G  SG+   ++E +  + +++L  +F+PFY RS + T+P+FLERRYN   R  L
Sbjct: 66  VSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRYNRACRDWL 125

Query: 120 SVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGMK 179
           + IS++S ++  +A +  AGG+V + +FGI         +++ + + +LT LYTI GG++
Sbjct: 126 AFISILSAIIIHIAFSFLAGGIVLETLFGID-------MYVSIVVIALLTGLYTIIGGLR 178

Query: 180 SVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDDA 239
           +V+ T  +Q+ +L+ G++II    + ++GGWD M  +   +   +  D ++ +    D +
Sbjct: 179 AVVVTETIQSLVLITGAIIITYFAWNKVGGWDHMTAI---LQKENAMDKLSMIRPIGDKS 235

Query: 240 NFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIPG 299
              W+   +G  ++G WYWC DQ IVQRVL  K+E  AR G++F  ++K+LPVF+F++PG
Sbjct: 236 GMSWIAVFLGYPVLGIWYWCADQTIVQRVLGAKDENHARVGSLFCGFIKILPVFIFVLPG 295

Query: 300 MIAFALHQ---------KYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVC 350
           + A+ L++         + +G+ GE  L        N    +  ++ +LLP G+ G++V 
Sbjct: 296 LFAYILYKSGTMDLSSLQTVGSNGETVL--------NTKGIYTLMITQLLPKGLVGILVA 347

Query: 351 GILAALMSSLASLFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWIPIM 410
            +L+ LMS +A   NS A L + D YKRF+PET +KKLV +G+ +  + + + I  +P++
Sbjct: 348 ALLSGLMSQIAGALNSIATLSSYDLYKRFKPETSDKKLVSVGRWSAGIALTVSIGLLPLL 407

Query: 411 RSVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVY 470
            S  + L+  + DV + +AP I   FLLG+ WK+ SA+G  + L+ G IIG         
Sbjct: 408 NSY-ESLFNGINDVIAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSIIGAGVFVVNKV 466

Query: 471 YSNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVFGTAT 530
           Y     +    F  + +         ++F  C+++ +V S         + + L + +  
Sbjct: 467 YGTETIIGQIPFMMMAF---------YLFCICVLIQVVFSHIYPVKHTAQSETLYWTSIW 517

Query: 531 KEQKAATRASWDHWDIIHTVIILAITGAFYWYF 563
           +  K+   +   ++  + +V++LAI G  Y YF
Sbjct: 518 EPLKSKGWSGIGNYKFL-SVLLLAIMGVLYVYF 549


Lambda     K      H
   0.328    0.142    0.454 

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: 913
Number of extensions: 52
Number of successful extensions: 7
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: 564
Length of database: 550
Length adjustment: 36
Effective length of query: 528
Effective length of database: 514
Effective search space:   271392
Effective search space used:   271392
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: 53 (25.0 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