GapMind for catabolism of small carbon sources

 

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

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Echvi_1871 Echvi_1871 transporter, SSS family

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Cola:Echvi_1871
          Length = 547

 Score =  593 bits (1528), Expect = e-174
 Identities = 294/547 (53%), Positives = 395/547 (72%), Gaps = 19/547 (3%)

Query: 11  IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70
           +D++VF  Y  +II +G+ VSR+KKG  K ++DYFLA K+LPWWAVGASLIA+NISAEQF
Sbjct: 6   LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQF 65

Query: 71  IGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTIL 130
           IGMSGSG+++GLAI++YEWM+A TL++V  +FLPI++++GIYT+P+F+ +R++ +++T++
Sbjct: 66  IGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTVM 125

Query: 131 AVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVWTDV 190
           A+FW+ +Y+FVNLTSVLYLG L+LETI+G+PL Y I+GLALFA+VYSIYGGL AV WTDV
Sbjct: 126 AIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWTDV 185

Query: 191 IQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQ-----------S 239
           +QV FLV GG  TTY+A+S +G  D W  G+  +  AAP HF MI+++           S
Sbjct: 186 VQVVFLVAGGLATTYLALSLVGDGDVW-EGIGILRKAAPSHFSMIIEKGEMMIPDGSGGS 244

Query: 240 NPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPF 299
              Y++LPG++VLIGG+W+ NL YWG NQYI QR LAAKS+ EAQ G+VFA FLKL++P 
Sbjct: 245 RDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMPL 304

Query: 300 LVVLPGIAAYVIT---SDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFA 356
           +VV+PGIAAYVI    +D   + S+ D     +   A +D+AYP L   LP G+KG+ FA
Sbjct: 305 IVVIPGIAAYVIVQKGADASFIESMTD----PVTGLAKSDRAYPTLLHLLPPGLKGLAFA 360

Query: 357 ALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPM 416
           AL AAIVSSLASM NST+TIFT+DIYKE+ + +  + K V +GR  AVVA IIA ++AP 
Sbjct: 361 ALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQ 420

Query: 417 LGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLS 476
           L  + QAFQYIQEYTG VSPG+ A+F+ G FWKKTTS  A+   V +IP +   K +  +
Sbjct: 421 LRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPN 480

Query: 477 MPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLA 536
           +PF+D+M    L   V+I   SL      D  K I V + +F T   F + A  I  +L 
Sbjct: 481 LPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILV 540

Query: 537 VLYTLFW 543
            LY++FW
Sbjct: 541 ALYSVFW 547


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: 962
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: 547
Length adjustment: 35
Effective length of query: 508
Effective length of database: 512
Effective search space:   260096
Effective search space used:   260096
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 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:

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:

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:

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:

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