GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Klebsiella michiganensis M5al

Align The glucose uptake porter, GluP (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter

Query= TCDB::Q0SE66
         (483 letters)



>FitnessBrowser__Koxy:BWI76_RS21205
          Length = 478

 Score =  303 bits (776), Expect = 9e-87
 Identities = 183/460 (39%), Positives = 267/460 (58%), Gaps = 25/460 (5%)

Query: 26  IAVVAALGGLLFGYDSAVINGAVSAIEGKFQV-DSALLGFAIASALLGAAAGAMLAGRIA 84
           I +VAA GGLLFGYD  VI GA    E  F + D A  G+A++SAL+G   GA+++G  A
Sbjct: 16  ICLVAACGGLLFGYDWVVIGGAKPFYEAWFSITDPAQSGWAMSSALVGCVFGALISGWCA 75

Query: 85  DRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAEISPA 144
           D+ GR + +  +AV+F  SA GT  A++ +M V +RIVGG+G+GLAS ++P YIAE+SPA
Sbjct: 76  DKLGRKLPLILSAVLFSASAWGTAVASSFDMFVVYRIVGGVGIGLASALSPLYIAEVSPA 135

Query: 145 RVRGRLGSLQQLAIVTGIFVSLLVDYALA--AIAGGSQE---ELWFGLEAWRWMFLAMCV 199
             RGR  ++ QL IV G+  + L++  +A     G +Q+   E W G   WRWMF A  V
Sbjct: 136 EKRGRFVAVNQLTIVIGVLAAQLINLMIAEPVATGATQQMIVETWNGQMGWRWMFGAELV 195

Query: 200 PALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSI 259
           PALA+ +L   +PESPR+L+  G+   AR  L  +      D  +  I  TL ++    +
Sbjct: 196 PALAFLVLMFFVPESPRWLMKAGKPERARAALERIGSADYADRILRDIAHTLEKDNH-KV 254

Query: 260 RDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVV 319
                 A  + PIV IG+ L+VFQQ+ GINVIF Y+  ++ + GFD  S+L+  V T VV
Sbjct: 255 SYGALLAPQVKPIVIIGMVLAVFQQWCGINVIFNYAQEIFASAGFDINSTLKSIVATGVV 314

Query: 320 NIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQG 379
           N+  TL A+  +D++GRR L+++G++G+ +    +A  +                 G+ G
Sbjct: 315 NLVFTLAALPLVDKIGRRKLMLLGASGLTLIYVLIAGAYA---------------MGIMG 359

Query: 380 PIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSM 439
              L+     +  + ++  PV WVLL E FPNR+R  A+SL   A W A +L+T TFP +
Sbjct: 360 WPVLLLVLAAIAIYALTLAPVTWVLLAEIFPNRVRGLAMSLGTLALWIACFLLTYTFP-L 418

Query: 440 KDFSLGISYGF--YAVCAVLSLVFVLRWVKETKGVELEAM 477
            +  LG +  F  Y V      +++LR V ETKGV LEA+
Sbjct: 419 LNAGLGAAGSFLLYGVICAAGYLYILRNVPETKGVTLEAL 458


Lambda     K      H
   0.324    0.138    0.405 

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: 588
Number of extensions: 27
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: 483
Length of database: 478
Length adjustment: 34
Effective length of query: 449
Effective length of database: 444
Effective search space:   199356
Effective search space used:   199356
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: 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:

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