Aligments for a candidate for SSS-glucose in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for SSS-glucose in Echinicola vietnamensis KMM 6221, DSM 17526

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Echvi_1880 Echvi_1880 transporter, SSS family

Query= SwissProt::P96169
         (543 letters)



>lcl|FitnessBrowser__Cola:Echvi_1880 Echvi_1880 transporter, SSS
           family
          Length = 624

 Score =  564 bits (1453), Expect = e-165
 Identities = 275/517 (53%), Positives = 377/517 (72%), Gaps = 17/517 (3%)

Query: 7   GLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANIS 66
           G S +D ++F +Y   I+ VGLWVSR KKG +K+ ++YFLA KSL WWAVGASL+AANIS
Sbjct: 4   GFSTLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANIS 63

Query: 67  AEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKL 126
           AE FIG SGSG++IGL I++YEW++AI LIIV KYFLPIF++ G+YT+P+F+ +RFNK +
Sbjct: 64  AEHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGV 123

Query: 127 KTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVV 186
            T  AVFW+ +Y+FVNLTSV YLG LAL+ I+GIPL Y I+GL +F+ +YSIYGGL AV 
Sbjct: 124 STAFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVA 183

Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQ-------- 238
           WTDV+QV  LV GG +TT++A+  +G  DG FAG+S + + A  HF MI+ Q        
Sbjct: 184 WTDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDG 243

Query: 239 ---SNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKL 295
              S   + +LPG+AV++GG+W+ NL YWGFNQYIIQ+ LAAKS+ EA+KG++FA +LKL
Sbjct: 244 LGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKL 303

Query: 296 IVPFLVVLPGIAAYVITSD--PQLMASLGDIAATNLPSAANADKAYPWLTQ-FLPVGVKG 352
           ++P +VV+PGIAAYV+ +D  P+ +A++ ++   ++ +   +D+AYPWL + F+P G++G
Sbjct: 304 LMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRG 363

Query: 353 VVFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACL 412
           + FAALAAAIVSSLASM+NST+TIFTMDIYK Y  P++ +H+LV  GR  AVVAL IA +
Sbjct: 364 LAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMI 423

Query: 413 IAPMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKF 472
           +AP L  + Q FQYIQEYTG + PG++ VF +GL W++ T+  A+   +A+IP  +  K 
Sbjct: 424 VAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVFKI 483

Query: 473 MPLSMPFMDQMLYT---LLFTMVVIAFTSLSTSINDD 506
               MPF+ +M Y    L F   +I+F       N D
Sbjct: 484 FYPEMPFLLRMGYVFIILCFIASLISFAEKKKFANPD 520



 Score = 44.3 bits (103), Expect = 1e-08
 Identities = 28/90 (31%), Positives = 50/90 (55%), Gaps = 8/90 (8%)

Query: 457 IIGVVASI-PFALFLKFMPLSMP--FMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISV 513
           I+G++ ++  FALF  +  + +   FM   L+ +L T   I +T++   +   DPK  + 
Sbjct: 539 ILGIICAVLGFALFNSYEHVGIESIFMIAALFLMLGT---ILYTNVK--METADPKSFNT 593

Query: 514 TSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543
              +F T  SFN+ A GI++++ +LY  FW
Sbjct: 594 DPVLFNTTSSFNLGAAGIILIVGLLYYFFW 623


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: 1171
Number of extensions: 53
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 543
Length of database: 624
Length adjustment: 36
Effective length of query: 507
Effective length of database: 588
Effective search space:   298116
Effective search space used:   298116
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:

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, or view the source code.

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