GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMIT1 in Pedobacter sp. GW460-11-11-14-LB5

Align Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 (characterized)
to candidate CA265_RS19720 CA265_RS19720 sodium transporter

Query= SwissProt::Q9JKZ2
         (718 letters)



>FitnessBrowser__Pedo557:CA265_RS19720
          Length = 558

 Score =  243 bits (621), Expect = 1e-68
 Identities = 159/501 (31%), Positives = 266/501 (53%), Gaps = 55/501 (10%)

Query: 4   VLEAADIAVVALYFILVMCIGFFAMWKSNRSTVSG---YFLAGRSMTWVAIGASLFVSNI 60
           +L+  D  V A+YF++V   G + ++   +S  +G   YFLA  S+TW AIGASL  SNI
Sbjct: 5   LLDTKDYIVFAIYFVIVAAYGLY-IYNKKKSASTGSKDYFLAEGSLTWWAIGASLIASNI 63

Query: 61  GSEHFIGLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGH 120
            +E FIG++GSG   G A+  +E+ A L L ++   FIP+Y+++ + TMP++L +R+ G 
Sbjct: 64  SAEQFIGMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRYNG- 122

Query: 121 RIQVYFAALSLLLYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVA 180
            + +  A   LLLY+   L+  LY GAL +    G++L   +  +     ++T+ GG+  
Sbjct: 123 TVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITL-GGMKV 181

Query: 181 VIYTDTLQALLMIIGALTLMVISMVKIGGFEEVKRRYMLASPDVASILLKYNLSNTNACM 240
           + YTD +Q   +I+G L    +++        V   Y       + I   Y+L  + A  
Sbjct: 182 IGYTDVIQVFFLILGGLATTYLAL------NLVSTHY-----GTSGIFEGYSLMTSKA-- 228

Query: 241 VHPKANALKMLRDPTDED-VPWPG---FILGQTPASVWYWCADQVIVQRVLAAKNIAHAK 296
               +    M+  P +E+ +  PG    + G    ++ YW  +Q I QR L A ++  A+
Sbjct: 229 ----SEHFHMILKPDNENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA-DLKTAR 283

Query: 297 GSTLMAGFLKLLPMFIIVVPGMISRIVFAD--------EIACINPEHCMQVCGSRAGCSN 348
           G  L A FLKLL   I+V+PG+ + +++ D        +   +NP+              
Sbjct: 284 GGILFAAFLKLLMPIIVVLPGIAAYVLYKDGAFQSEMLQDGSVNPDR------------- 330

Query: 349 IAYPRLVMTLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKS-ASSREL 407
            AYP +++ L+P GL+GL  A + AA+++ L    NS +TIFTLD+YK + K+ AS + L
Sbjct: 331 -AYP-VLLNLLPAGLKGLSFAALTAAVVASLAGKANSIATIFTLDIYKKVLKTDASEKNL 388

Query: 408 MIVGRIFVAFMVVISIAWVPII-VEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCN 466
           +  G+I V   +V+ +   P + ++ +GG  + YIQE   +++P + A+F+L  FWKR  
Sbjct: 389 VFTGKIAVVVAMVLGVVIAPYLGIDKKGG--FQYIQEYTGFVSPGIFAMFILGFFWKRAT 446

Query: 467 EQGAFYGGMAGFVLGAVRLIL 487
              A +  + GF L  +  +L
Sbjct: 447 SNAALFATVGGFGLSLLLKVL 467


Lambda     K      H
   0.326    0.139    0.420 

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: 1019
Number of extensions: 50
Number of successful extensions: 9
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: 718
Length of database: 558
Length adjustment: 38
Effective length of query: 680
Effective length of database: 520
Effective search space:   353600
Effective search space used:   353600
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: 54 (25.4 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