GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SOT in Klebsiella michiganensis M5al

Align Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= TCDB::AIU41385.1
         (509 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS24055 BWI76_RS24055 MFS
           transporter
          Length = 464

 Score =  234 bits (597), Expect = 5e-66
 Identities = 139/453 (30%), Positives = 243/453 (53%), Gaps = 25/453 (5%)

Query: 33  LASMTSILLGYDIGVMSGASIYIQEDLKISDVEVEILIGILNLYSLIGSAAAGRTSDWIG 92
           LA++  +L G DIGV++GA  +I  + +IS    E ++  +   + +G+  +G  S  +G
Sbjct: 21  LAALAGLLFGLDIGVIAGALPFIANEFQISAHTQEWVVSSMMFGAAVGAVGSGWLSFKLG 80

Query: 93  RRYTIVFAGAIFFTGALLMGFATNYAFLMVGRFVAGIGVGYALMIAPVYNAEVSPASSRG 152
           R+ +++    +F  G+L    A N   L++ R + G+ VG A   AP+Y +E++P   RG
Sbjct: 81  RKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAPLYLSEIAPEKIRG 140

Query: 153 ALTSFPEVFVNIGILLGYVANYAFSGLPINLGWRLMLGVGVFPSVILAVGVLTMPESPRW 212
           ++ S  ++ + IGIL  Y+++ AFS    +  WR MLGV + P+V+L +GV+ +P+SPRW
Sbjct: 141 SMISMYQLMITIGILGAYLSDTAFS---YSGAWRWMLGVIIIPAVLLLIGVVFLPDSPRW 197

Query: 213 LVMQGRLGDAKHVLDKTSDSLEEAQLRLADIKEAAGIPEHCTEDVVQVPKHSHGEEVWKE 272
              + R  DA+ VL +  D+  EA+  L +I+E+  + +              G  ++KE
Sbjct: 198 FAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLKVKQ-------------SGWSLFKE 244

Query: 273 LLLHPTPPVRHILIAAVGFHFFQQMSGIDALVLYSPRIFRASGITDSSTLLLATVAVGFS 332
                    R  +   V     QQ +G++ ++ Y+P+IF  +G  +++  +  TV VG +
Sbjct: 245 -----NSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTVIVGLT 299

Query: 333 KTIFTLIAIGFLDRVGRRPLLLTSVAGMIASLLCLGTSLTIVDHEKEKMMWASVVCLTMV 392
             + T IAIG +DR GR+P L+     M   +  LG+ + I  H      +A    + M+
Sbjct: 300 NVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMHIGIHSATAQYFA----VLML 355

Query: 393 LAYVGFFSIGMGPIAWVYSSEIFPLKLRAQGCSMGTAVNRIMSGVLTMTFITLYKAITMG 452
           L ++  F++  GP+ WV  SEI PLK R  G +  TA N I + ++  TF+T+  ++   
Sbjct: 356 LMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLGSA 415

Query: 453 GTFFLYGAIATVGWVFFYTMLPETQGRTLEDME 485
            TF++YG +  +       ++PET+  +LE +E
Sbjct: 416 NTFWVYGGLNILFIFLTLWLIPETKNVSLEHIE 448


Lambda     K      H
   0.326    0.140    0.424 

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: 681
Number of extensions: 46
Number of successful extensions: 4
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: 509
Length of database: 464
Length adjustment: 34
Effective length of query: 475
Effective length of database: 430
Effective search space:   204250
Effective search space used:   204250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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