GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3610523 Dshi_3904 SSS sodium solute
           transporter superfamily (RefSeq)
          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 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