GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SOT in Sphingomonas koreensis DSMZ 15582

Align Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= TCDB::AGG19156.1
         (491 letters)



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

 Score =  228 bits (582), Expect = 3e-64
 Identities = 149/456 (32%), Positives = 239/456 (52%), Gaps = 43/456 (9%)

Query: 4   ILLGYDIGVMSGAAIYIEKDLKVTDTQIEILLGILNLYSLIGSAMAGRTSDWVGRRYTIV 63
           +L G+D  V+SGA   ++    +TD  +   +    + +++GS +AG  +D  GR+  ++
Sbjct: 34  LLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGRKGVML 93

Query: 64  ISGAIFFTGAILMGLSTNYTFLMCGRFVAGLGVGYALTIAPVYAAEVSPASSRGFLTSFP 123
                +   ++  GL+ +    +  RF+ GL +G A  + P+Y AEVSPA  RG L +  
Sbjct: 94  TVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGRLVAMN 153

Query: 124 EVFVNVGILLGYISNYAFS-FCALDLGWRLMLGVGAIPSVILAIGVLAMPESPRWLVMQG 182
           ++ + +GIL+ ++SNY  +     D+ WR M G+ A+PS I  +  L +PESPRWL + G
Sbjct: 154 QLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHG 213

Query: 183 RLGDARQVLDKT--SDSKEE-SMLRLADIK-EAAGIPEDCNDDIVQVTGHSHGEGVWKEL 238
           +   AR V+ +   +D + E + + LA+ + EAAG P                      L
Sbjct: 214 QADRARDVMQRLGFADPRAELARIELAEAREEAAGKP---------------------RL 252

Query: 239 F--VHPTPTVLHILIAALGFHFFQQASGIDALVLYSPRVFEKAGITSSDQLLLCTVGVGL 296
           F   H TP    I IA      F Q SGI+AL+ Y+PR+FE AG   +D  LL ++ VG 
Sbjct: 253 FQRSHFTPVACAIAIA-----MFNQLSGINALLYYAPRIFELAG-AGADSALLQSIAVGG 306

Query: 297 SKTVFTLVATFFLDRVGRRPLLLTSMAGMVVSLVCLGTSLTIVDQHEGARMTWAVVLCLF 356
           +  VFT+ A F +DR GRRPLL       V S++C  T L +  Q E A+    ++  LF
Sbjct: 307 TNLVFTVAALFLIDRFGRRPLL------FVGSVICAATLLLVGWQLESAKPDGTLI--LF 358

Query: 357 CVLAFVGFFSTGIGPIAWVYSSEIFPLRLRAQGCGMGVAVNRVMSGILSMTFISLYKAIT 416
            +L F+  F+   G + WV+ SE+FP  +R +G  +G   + VM+  ++  F  ++ A  
Sbjct: 359 GLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAF-PVFAASV 417

Query: 417 MGGAFFLYAAIGAVGWIFFFTMLPETQGRTLEDMEV 452
            G  F  + A+  +  ++ +  +PET G  LEDM +
Sbjct: 418 GGWVFAFFGAMMLLQLLWTWKFMPETNGIALEDMNL 453


Lambda     K      H
   0.326    0.141    0.428 

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: 601
Number of extensions: 38
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: 491
Length of database: 458
Length adjustment: 33
Effective length of query: 458
Effective length of database: 425
Effective search space:   194650
Effective search space used:   194650
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: 51 (24.3 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