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

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_RS06755 CA265_RS06755 sodium transporter

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Pedo557:CA265_RS06755
          Length = 542

 Score =  517 bits (1331), Expect = e-151
 Identities = 260/546 (47%), Positives = 365/546 (66%), Gaps = 17/546 (3%)

Query: 8   LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67
           LS  D  VF +Y  I+   G WV R KK  +  T+DYFLA  SL WWA+GAS+IA+NISA
Sbjct: 4   LSAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASNISA 63

Query: 68  EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127
           E FIGMSGSG+++GLAIASYEWM+A TLIIV  +FLPI+I+  IYT+P+F+  R+N  + 
Sbjct: 64  EHFIGMSGSGFAMGLAIASYEWMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNNTVS 123

Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVW 187
           T++AVFW+ +Y+FVNLTS+ +LG +A+ETI G+P    I+ LA+F+ + ++ GG+  + +
Sbjct: 124 TLMAVFWLLVYVFVNLTSIFFLGAIAIETITGVPFNICIIFLAIFSAIITL-GGMKVIGY 182

Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIG---GTDGWFAGVSKMVDAAPGHFEMILDQSNPQYM 244
           TDVIQVF LV GG +T YMA+  +          A +  +   A  HF MI  + +  Y 
Sbjct: 183 TDVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHMIFSKGDKFYN 242

Query: 245 NLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLP 304
            LPGIAVL+GGLW+ NL YWG NQYI+QR L A  +   + G++FAAFLKL++P +VV+P
Sbjct: 243 ELPGIAVLVGGLWINNLNYWGCNQYIVQRALGA-DLKTGRNGLIFAAFLKLLIPVIVVIP 301

Query: 305 GIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVS 364
           GIAAYV+       + + D A    P     D AYP L   LP G+KG+ FAAL AAIV+
Sbjct: 302 GIAAYVLYQRGYFHSEMLDAAGVVKP-----DHAYPVLMNLLPAGIKGLAFAALTAAIVA 356

Query: 365 SLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAF 424
           SLA   NS ATIFT+DIYK++I P++ + +LV+VGR + V+A +IA +IAP L    Q +
Sbjct: 357 SLAGKCNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLIAIIIAPALRSFDQVY 416

Query: 425 QYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMP-------LSM 477
           Q+IQEY G +SPG+ A+FLLG FWKKTTS+ A+   + +IP +   KF+P         +
Sbjct: 417 QFIQEYVGFISPGVFAIFLLGFFWKKTTSRAALTAALLTIPLSTLFKFLPAVTNGAIAPI 476

Query: 478 PFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAV 537
           PF+++M +  +  + ++   +L+   + D+P+G+ + SSMF    +F IA+  I  +LA 
Sbjct: 477 PFLNRMSWVFMIIIGLMIVVTLTDPKSKDNPQGLEIDSSMFKVTPAFTIASVMICGILAA 536

Query: 538 LYTLFW 543
           LYT+FW
Sbjct: 537 LYTVFW 542


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: 930
Number of extensions: 41
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: 543
Length of database: 542
Length adjustment: 35
Effective length of query: 508
Effective length of database: 507
Effective search space:   257556
Effective search space used:   257556
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources