Alignments for a candidate for SGLT1 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for SGLT1 in Echinicola vietnamensis KMM 6221, DSM 17526

Align sodium/glucose cotransporter 1 (characterized)
to candidate Echvi_1871 Echvi_1871 transporter, SSS family

Query= CharProtDB::CH_091086
         (664 letters)



>FitnessBrowser__Cola:Echvi_1871
          Length = 547

 Score =  257 bits (656), Expect = 1e-72
 Identities = 172/523 (32%), Positives = 282/523 (53%), Gaps = 34/523 (6%)

Query: 25  NAADISIIVIYFVVVMAVGLWAMFSTNRGTVGG---FFLAGRSMVWWPIGASLFASNIGS 81
           N  D+ + V Y ++++ +G+  +    +G V     +FLA +++ WW +GASL ASNI +
Sbjct: 4   NTLDLVVFVAYCLLIITMGI-VVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISA 62

Query: 82  GHFVGLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRI 141
             F+G++G+G A G+AI  +EW A   ++V+   F+PIY+K G+ TMP++L +R+ G R+
Sbjct: 63  EQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDG-RV 121

Query: 142 QVYLSLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVI 201
           +  +++  LL+Y+F  +++ ++ GA+ +   +G+ L   I  L     +Y+I GGL AV 
Sbjct: 122 RTVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVA 181

Query: 202 YTDTLQTVIMLVGSLILTGFAFHEVGGYDAF--MEKYMKAIPTIVSDGNTTFQEKCYTPR 259
           +TD +Q V ++ G L  T  A   VG  D +  +    KA P+  S       EK     
Sbjct: 182 WTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFS----MIIEKGEMMI 237

Query: 260 ADSFHIFRDPLTGDLPWPG-FIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCG 318
            D     RD    DLP     I GM I+ L YW  +Q I QR L+AK++   + G +  G
Sbjct: 238 PDGSGGSRDAYL-DLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAG 296

Query: 319 YLKLMPMFIMVMPGMISRILYTEKI-ACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNG 377
           +LKL+   I+V+PG+ + ++  +   A  + S  +   G  +  ++ AYPTL + L+P G
Sbjct: 297 FLKLLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTG--LAKSDRAYPTL-LHLLPPG 353

Query: 378 LRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYAK-VRKRASEKELMIAGRLFILVLIGI 436
           L+GL  + + A+++SSL S+ NS ST+FT+DIY +   K  SE + +  GR  I  ++  
Sbjct: 354 LKGLAFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGR--ITAVVAF 411

Query: 437 SIAWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGL-LI 495
            IA +   Q  Q  Q F YIQ  T ++ P + A+F+   FWK+     A    +L + L 
Sbjct: 412 IIAAIVAPQLRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLS 471

Query: 496 GISRMITEFAYGTGSCMEPSNCPTI-ICGVHYLYFAIILFAIS 537
              ++IT             N P I   GV +L  ++++ AIS
Sbjct: 472 AAFKVIT------------PNLPFIDRMGVVFLVLSVLIIAIS 502


Lambda     K      H
   0.327    0.141    0.436 

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: 710
Number of extensions: 29
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: 664
Length of database: 547
Length adjustment: 37
Effective length of query: 627
Effective length of database: 510
Effective search space:   319770
Effective search space used:   319770
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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