Alignments for a candidate for SSS-glucose in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for SSS-glucose in Stenotrophomonas chelatiphaga DSM 21508

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate WP_057509052.1 ABB28_RS13160 sodium transporter

Query= SwissProt::P96169
         (543 letters)



>NCBI__GCF_001431535.1:WP_057509052.1
          Length = 520

 Score =  540 bits (1392), Expect = e-158
 Identities = 270/537 (50%), Positives = 371/537 (69%), Gaps = 20/537 (3%)

Query: 8   LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67
           LS +D  +  +Y+A +  +  WVSR+K G  K  +DYFLA KSLPWWAVGASLIAANISA
Sbjct: 3   LSVLDTSIVLVYLAGVFVLAQWVSREKAGHAKDAKDYFLASKSLPWWAVGASLIAANISA 62

Query: 68  EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127
           EQ IGMSGSGY+IGLAIASYEWM+A+TL+IVGK+FLP+F+  GIYT+P+F+E+R+  +++
Sbjct: 63  EQIIGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPVFLRNGIYTMPQFLEQRYGTRIR 122

Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVW 187
           T++AVFW+ LY+FVN+TS+L+LG +A+  + G+  M +++ + +FAL+Y +YGGL AV  
Sbjct: 123 TLMAVFWLGLYVFVNVTSILWLGAIAVSQVTGMDQMLAVVLIGVFALLYQLYGGLKAVAL 182

Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLP 247
           TD++QV  LVLGG + T + +S +G   G  AG+ ++ +A PGHFEMIL + N  Y +LP
Sbjct: 183 TDIVQVSLLVLGGLLVTGLTLSQLGEGAGIVAGMQRLWEAHPGHFEMILSKDNLFYKDLP 242

Query: 248 GIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIA 307
           GI+VL+GGLW+ NL YWGFNQYIIQR LAAK + EAQKG++FAAFLKL++P +VV+PGIA
Sbjct: 243 GISVLVGGLWIMNLSYWGFNQYIIQRALAAKDIGEAQKGVLFAAFLKLLMPLIVVVPGIA 302

Query: 308 AYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLA 367
           A ++                  P     D+AYP + + LP G+ G+VFAAL AAIV+SLA
Sbjct: 303 AVMLA-----------------PGLDAPDQAYPTMMRLLPTGILGMVFAALVAAIVASLA 345

Query: 368 SMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIA-PMLGGIGQAFQY 426
           S +NS ATIFT+D Y +   P   +  LV VGR AA V +++  L A P+LG   QAFQY
Sbjct: 346 SKINSVATIFTLDFYAQRKGPHD-EATLVRVGRIAAAVTVVLGILAAKPLLGSFDQAFQY 404

Query: 427 IQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFMDQMLYT 486
           IQEYTG  +PGI+ +FLLGLFWK+    GA+   V S   ++ LK    S+PF+D++   
Sbjct: 405 IQEYTGFFTPGIVVIFLLGLFWKRANEAGALAAAVGSFVLSVVLKLAWPSLPFIDRVGLV 464

Query: 487 LLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543
            L  +++    SL+T         +     ++ T  SFN+ A  ++ +L  LYTLFW
Sbjct: 465 FLLALLLAVGVSLATPAAPAKDV-VRTDDVVYATRPSFNVGAIAVVAILIALYTLFW 520


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: 967
Number of extensions: 46
Number of successful extensions: 5
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: 520
Length adjustment: 35
Effective length of query: 508
Effective length of database: 485
Effective search space:   246380
Effective search space used:   246380
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

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 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