GapMind for catabolism of small carbon sources

 

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

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate CA265_RS19720 CA265_RS19720 sodium transporter

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Pedo557:CA265_RS19720
          Length = 558

 Score =  504 bits (1297), Expect = e-147
 Identities = 259/557 (46%), Positives = 362/557 (64%), Gaps = 33/557 (5%)

Query: 12  DIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQFI 71
           D +VFAIY  I+   GL++   KK     ++DYFLA  SL WWA+GASLIA+NISAEQFI
Sbjct: 10  DYIVFAIYFVIVAAYGLYIYNKKKSASTGSKDYFLAEGSLTWWAIGASLIASNISAEQFI 69

Query: 72  GMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTILA 131
           GMSGSG+ +GLAIA+YEWM+A+TL+IV  +F+P++++  I T+P+F+ +R+N  +  I+A
Sbjct: 70  GMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRYNGTVAMIMA 129

Query: 132 VFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVWTDVI 191
           VFW+ LY+ VNLTS+LYLG LA+ +I G  L + +  +A FA+V ++ GG+  + +TDVI
Sbjct: 130 VFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITL-GGMKVIGYTDVI 188

Query: 192 QVFFLVLGGFMTTYMAVSFIG---GTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLPG 248
           QVFFL+LGG  TTY+A++ +    GT G F G S M   A  HF MIL   N  Y++LPG
Sbjct: 189 QVFFLILGGLATTYLALNLVSTHYGTSGIFEGYSLMTSKASEHFHMILKPDNENYIDLPG 248

Query: 249 IAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIAA 308
           ++VL+GG+W+ NL YWG NQYI QR L A  +  A+ GI+FAAFLKL++P +VVLPGIAA
Sbjct: 249 LSVLVGGMWIVNLNYWGCNQYITQRALGA-DLKTARGGILFAAFLKLLMPIIVVLPGIAA 307

Query: 309 YVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLAS 368
           YV+  D    + +          + N D+AYP L   LP G+KG+ FAAL AA+V+SLA 
Sbjct: 308 YVLYKDGAFQSEMLQ------DGSVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLAG 361

Query: 369 MLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLG-GIGQAFQYI 427
             NS ATIFT+DIYK+ +  D+ +  LV  G+ A VVA+++  +IAP LG      FQYI
Sbjct: 362 KANSIATIFTLDIYKKVLKTDASEKNLVFTGKIAVVVAMVLGVVIAPYLGIDKKGGFQYI 421

Query: 428 QEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMP------------- 474
           QEYTG VSPGI A+F+LG FWK+ TS  A+   V     +L LK +P             
Sbjct: 422 QEYTGFVSPGIFAMFILGFFWKRATSNAALFATVGGFGLSLLLKVLPTWTDLSWLSGMGF 481

Query: 475 --------LSMPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNI 526
                     +PF+D+M +  +F ++ +   SL  + N  +PKG+ + S MF T   F +
Sbjct: 482 SVKNGVGVYEIPFLDRMGFVFVFCVIGMVIISLFENRNGVNPKGLEIDSKMFKTTTGFAV 541

Query: 527 AAYGIMIVLAVLYTLFW 543
            +  I+ +L  LY+++W
Sbjct: 542 GSLIIIGLLVALYSVYW 558


Lambda     K      H
   0.326    0.141    0.421 

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: 44
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: 543
Length of database: 558
Length adjustment: 36
Effective length of query: 507
Effective length of database: 522
Effective search space:   264654
Effective search space used:   264654
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