GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HMIT in Sphingomonas koreensis DSMZ 15582

Align Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= SwissProt::Q921A2
         (637 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1777 Ga0059261_1777 MFS
           transporter, sugar porter (SP) family
          Length = 458

 Score =  176 bits (446), Expect = 2e-48
 Identities = 125/365 (34%), Positives = 183/365 (50%), Gaps = 25/365 (6%)

Query: 45  AASLQGAELERAARRQFQRDETPAFVYAAAAFSALGGFLFGYDTGVVSGAMLLLRRQMRL 104
           +AS  GA  E A         T A + +AA  +ALGG LFG+DT V+SGA   L+ Q  L
Sbjct: 5   SASFAGAPDEEARA-------TVAIILSAAG-AALGGLLFGFDTAVISGATQALQLQFGL 56

Query: 105 GAMWQELLVSGAVGAAAVAALAGGALNGALGRRSAILLASALCTVGSAVLAAAANKETLL 164
                   V+ A+    + +L  GA     GR+  +L  +    V S     A +    L
Sbjct: 57  TDAMLGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFL 116

Query: 165 AGRLVVGLGIGIASMTVPVYIAEVSPPNLRGRLVTINTLFITGGQFFA----SVVDGAFS 220
             R + GL IG AS+  P+YIAEVSP   RGRLV +N L I  G   A     ++ G   
Sbjct: 117 VFRFMGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQ 176

Query: 221 YLQKDGWRYMLGLAAIPAVIQFLGFLFLPESPRWLIQKGQTQKARRILSQMRGNQTIDEE 280
           Y     WR+M G+ A+P+ I  L  L LPESPRWL   GQ  +AR ++ ++      D  
Sbjct: 177 Y--DVAWRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRL---GFADPR 231

Query: 281 YDSIRNSIEEEEKEASAAGPIICRMLSYPPTRRALAVGCGLQMFQQLSGINTIMYYSATI 340
            +  R  + E  +EA A  P + +   + P   A+A+     MF QLSGIN ++YY+  I
Sbjct: 232 AELARIELAEAREEA-AGKPRLFQRSHFTPVACAIAIA----MFNQLSGINALLYYAPRI 286

Query: 341 LQMSGVEDDRLAIWLASITAFTNFIFTLVGVWLVEKVGRRKLTFGSLAGTTVALTILALG 400
            +++G   D  A+  +     TN +FT+  ++L+++ GRR L F  +     A T+L +G
Sbjct: 287 FELAGAGADS-ALLQSIAVGGTNLVFTVAALFLIDRFGRRPLLF--VGSVICAATLLLVG 343

Query: 401 FLLSA 405
           + L +
Sbjct: 344 WQLES 348



 Score = 43.9 bits (102), Expect = 2e-08
 Identities = 25/96 (26%), Positives = 45/96 (46%), Gaps = 1/96 (1%)

Query: 499 LVGLVLYLVFFAPGMGPMPWTVNSEIYPLWARSTGNACSAGINWIFNVLVSLTFLHTAEY 558
           L GL+ ++  FA   G + W   SE++P   R  G A  +  +W+    ++  F   A  
Sbjct: 357 LFGLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAAS 416

Query: 559 LTYYGAFFLYAGFAAVGLLFVYGCLPETKGKKLEEI 594
           +  +  F  +     + LL+ +  +PET G  LE++
Sbjct: 417 VGGW-VFAFFGAMMLLQLLWTWKFMPETNGIALEDM 451


Lambda     K      H
   0.322    0.136    0.410 

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: 568
Number of extensions: 26
Number of successful extensions: 6
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: 637
Length of database: 458
Length adjustment: 35
Effective length of query: 602
Effective length of database: 423
Effective search space:   254646
Effective search space used:   254646
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 preprint 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