GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Dinoroseobacter shibae DFL-12

Align sodium/glucose cotransporter 1 (characterized)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)

Query= CharProtDB::CH_091086
         (664 letters)



>FitnessBrowser__Dino:3610525
          Length = 533

 Score =  292 bits (748), Expect = 2e-83
 Identities = 179/541 (33%), Positives = 298/541 (55%), Gaps = 53/541 (9%)

Query: 28  DISIIVIYFVVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGL 87
           D +I+VIYF+ V+A G++       G   G+FLAGRS+ W+ IG SLFASN+    FVGL
Sbjct: 12  DYAIVVIYFIGVIAHGVYVSRKNEEGA-DGYFLAGRSLPWYLIGFSLFASNMSGSSFVGL 70

Query: 88  AGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYLSL 147
            G   A+GI I  +EW A +++++     +P ++KA + T+PE+L +R+  +  + + S+
Sbjct: 71  MGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYDVRSRRAF-SI 129

Query: 148 LSLLLYIFTKISADIFSGAIFINLALG-LNLYLAIFLLLAITALYTITGGLAAVIYTDTL 206
            ++L  +F   +  +++G + I+   G LNL+ A+ +L  +  +YTI GGL+AV+ TDT+
Sbjct: 130 FTILAILFIDTAGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTILGGLSAVVVTDTV 189

Query: 207 QTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPRADSFHIF 266
           Q +++++G+ IL      E+GG+    E+    IP    +G+    ++   P  D F   
Sbjct: 190 QAILLIIGAAILFWLGLDEIGGW----EQLFVDIP----EGH----DQLILPADDDF--- 234

Query: 267 RDPLTGDLPWPGFIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCGYLKLMPMF 326
                  LPW G ++G+ +L  +YW  +Q +VQR L AKN+   + G +  G+LKL  +F
Sbjct: 235 -------LPWTG-LWGVVLLGFYYWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPNIF 286

Query: 327 IMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLRGLMLSVM 386
           +M++PG+I+  LY E                 +   ++A+PTL  ELMP G+RGL+++ +
Sbjct: 287 LMIIPGVIALKLYPE-----------------LETPDLAFPTLAFELMPIGVRGLIMAAL 329

Query: 387 LASLMSSLTSIFNSASTLFTMDIYAKVRKRASEKELMIAGRLFILVLIGISIAWVPIVQS 446
           +A++MSSL S  NSASTL   D    + +    K++ I GRL    ++     + P +  
Sbjct: 330 IAAIMSSLDSAMNSASTLVVKDFVEPIWEVDEGKQVWI-GRLVTGAVMVFGAIYAPSIAG 388

Query: 447 AQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGLLIGISRMITEFAY 506
            +S  LF Y QS  SY+ P I  V+++ +F   +N  GAFW +ILGL++GI   I +   
Sbjct: 389 FES--LFSYFQSSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGIPLFIMKEVT 446

Query: 507 GTGSCMEPSNCPTIICGVHYLYFAIILFAISFITIVVISLLTKPIPDVHLYRLCWSLRNS 566
           G  + M        +  +HY   + ++  +   T   IS LT+     ++  L WS  ++
Sbjct: 447 GVWAGMG-------LPEIHYTIMSTLMMCLGLATHFGISALTRKADKENIEDLVWSAADT 499

Query: 567 K 567
           K
Sbjct: 500 K 500


Lambda     K      H
   0.327    0.141    0.436 

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: 845
Number of extensions: 42
Number of successful extensions: 6
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: 664
Length of database: 533
Length adjustment: 37
Effective length of query: 627
Effective length of database: 496
Effective search space:   310992
Effective search space used:   310992
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