GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sglS in Dinoroseobacter shibae DFL-12

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Dino:3610523
          Length = 526

 Score =  263 bits (673), Expect = 9e-75
 Identities = 173/556 (31%), Positives = 289/556 (51%), Gaps = 50/556 (8%)

Query: 4   IEHGLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAA 63
           I+  L+ +D  V A+Y+AI+I +G+WV+R  +    + ED FLAG+SL W A+G SL A+
Sbjct: 5   IDANLTMLDYGVIAVYLAIVIAIGVWVARKTR----TGEDLFLAGRSLGWAAIGFSLFAS 60

Query: 64  NISAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFN 123
           NIS    +G++GS Y+ GL ++SYEWM+ I L+ +   F P+F++  I T PE++E R++
Sbjct: 61  NISTSTLVGLTGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYS 120

Query: 124 KKLKTILAVFWISLYIFVNLTSVLYLGGLALETIL-GIPLMYSILGLALFALVYSIYGGL 182
           ++++   +   I   + V+    LY G + L+     + +  S + + LFA +Y+  GGL
Sbjct: 121 RRVRLYFSGLTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGL 180

Query: 183 SAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQ 242
            AVV+TD++Q   L+ G  +T ++    +      F+  S       GH   I+   +  
Sbjct: 181 RAVVYTDILQAVVLICGTGLTAFLMYQSVD-----FSWESVRSQVPEGHLS-IVQPIDDD 234

Query: 243 YMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVV 302
            +  PG   L  G+W+   +YW  NQYI+QR L AK +S AQ G +    LK++  F ++
Sbjct: 235 TLPWPG---LFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTFFII 291

Query: 303 LPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYP-WLTQFLPVGVKGVVFAALAAA 361
           LPG+ A V                  LP   N+D+ +P  +T+ LP G+ G+V A L AA
Sbjct: 292 LPGVMALV-----------------TLPDIQNSDQVFPIIITEVLPSGLTGLVMAGLIAA 334

Query: 362 IVSSLASMLNSTATIFTMD-IYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGI 420
           I+S++ S LNS++T+   D + +    PD    K    G  A +  ++IA   AP++   
Sbjct: 335 IMSTVDSTLNSSSTLLINDFLTRPEKEPDPETAK--KWGMMATLGFMVIAIAWAPLIQYF 392

Query: 421 GQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFM 480
           G  + YIQ+   ++ P ++  F LG  W + T   A   ++  I   L L    L+   +
Sbjct: 393 GGLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLI--IGHTLGLVVFMLNQFGI 450

Query: 481 DQMLYTLLFTMV--VIAFTSLSTSINDDDP----KGISVTSSMFVTDRSF-----NIAAY 529
             + YT+  T++  V A   ++ S+ DD P      +   +  F T  +      N+  +
Sbjct: 451 WPLHYTISVTIMTAVSAAIFVALSLRDDTPDVREDALWQRADAFDTPATTAPVLKNVKTH 510

Query: 530 GIMIVLAVLYT--LFW 543
            I+++L ++ T  LFW
Sbjct: 511 AILLILLMIGTLVLFW 526


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: 890
Number of extensions: 39
Number of successful extensions: 7
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: 526
Length adjustment: 35
Effective length of query: 508
Effective length of database: 491
Effective search space:   249428
Effective search space used:   249428
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