Alignments for a candidate for SMIT1 in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for SMIT1 in Sphingomonas koreensis DSMZ 15582

Align Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rKST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate Ga0059261_1623 Ga0059261_1623 transporter, SSS family

Query= SwissProt::Q28728
         (674 letters)



>FitnessBrowser__Korea:Ga0059261_1623
          Length = 549

 Score =  260 bits (664), Expect = 1e-73
 Identities = 169/496 (34%), Positives = 271/496 (54%), Gaps = 55/496 (11%)

Query: 23  SLEPGDIAVLVLYFLFVLAVGLWSTVKTK---RDTVKGYFLAGGDMVWWPVGASLFASNV 79
           SL   D+ V+++Y + + A+  W + +     +DT   YFLA   + WW +GASL A+N+
Sbjct: 3   SLSHIDLIVVIVYAIGIFALAQWVSREKAGHAKDT-SDYFLASKSLPWWAIGASLIAANI 61

Query: 80  GSGHFVGLAGSGAATGISVAAYEFNGMFSVLMLAWIFLPIYIAGQVTTMPEYLRRRFGGS 139
            +   VG++GSG A G+++A+YE+    ++L++   FLPI++  ++ TMP++L +RFG +
Sbjct: 62  SAEQIVGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPIFLKNEIYTMPQFLEQRFGPT 121

Query: 140 RIAITLAVLYLFIYIFTKISVDMYAGAIFIQQSLHLDLYLSVVGLLAVTALYTVAGGLAA 199
            I   +AV +L +YIF  ++  ++ G+I + Q   +D  +++ GL A   +Y + GGL A
Sbjct: 122 -IRTVMAVFWLALYIFVNLTSILWLGSIAVTQVAGVDQDIALFGLGAFALVYQLRGGLKA 180

Query: 200 VIYTDALQTLIMLVGALTLMGYSFAAVGGMEGLQEKYFLALPSNRSENSSCGLPREDAFH 259
           V  TD +Q  ++++G L +   + + +GG  G+   +            +  LP +    
Sbjct: 181 VALTDIVQVTLLVLGGLVISYLTLSKIGGDAGVMGGF---------TRLTTELPGKFDMI 231

Query: 260 LFRD-PLTSDLPWPGILF-GMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKV 317
           L  D P   DLP   +L  GM I +L YW  +Q I+QR+LAAK+LS A+ G + AA+LK+
Sbjct: 232 LAPDNPFYKDLPGLSVLIGGMWIANLSYWGFNQYIIQRALAAKSLSEAQKGVVFAAFLKL 291

Query: 318 LPLFIMVFPGMVSRILFPDQVACADPETCQRVCNNPSGCSDIAYPKLVLELLPTGLRGLM 377
           L   I+V PG+ + IL PD    A P              D AYP + + LLP GL GL+
Sbjct: 292 LMPVIIVLPGIAAVILAPD---LAKP--------------DQAYPTM-MRLLPVGLLGLV 333

Query: 378 MAVMVAALMSSLTSIFNSASTIFTMDLWNHVR--------------------PRASEKEL 417
            A +VAA+++S  S  NS +TIFT+DL+   +                      A EK+L
Sbjct: 334 FAALVAAIIASTASKINSIATIFTLDLYAKAKGVQSRAQDAATASASGDSGLTAAHEKQL 393

Query: 418 MIVGRVFVLLLVLVSVLWIPVVQASQGGQLFVYIQAISSYLQPPVAMVFVLGCFWKRANE 477
           + VGR   ++  L+++     +  S   Q F YIQ  S ++ P + ++F+LG FW RA E
Sbjct: 394 VRVGRTTAVVATLLAIFTARPLLGSL-DQAFQYIQEFSGFVTPGITVIFLLGLFWPRATE 452

Query: 478 KGAFWGLVLGLLLGFI 493
            GA  G V  +LL F+
Sbjct: 453 AGALTGAVASVLLSFL 468


Lambda     K      H
   0.325    0.138    0.426 

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: 742
Number of extensions: 38
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: 674
Length of database: 549
Length adjustment: 37
Effective length of query: 637
Effective length of database: 512
Effective search space:   326144
Effective search space used:   326144
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. 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 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