GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcP in Klebsiella michiganensis M5al

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter

Query= TCDB::P15729
         (468 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS03110 BWI76_RS03110 MFS
           transporter
          Length = 499

 Score =  265 bits (678), Expect = 2e-75
 Identities = 162/477 (33%), Positives = 257/477 (53%), Gaps = 26/477 (5%)

Query: 1   MNPSSSPSQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSV 60
           +N +S P+  T    FV +++ +A LGG LFG+DT VI+GA+  +          TGL  
Sbjct: 9   LNKASGPNSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVT 68

Query: 61  SLALLGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIG 120
           S  L G+A GA  +G +A+  GR K ++  AVLF + +IG+ +   +   IF+R++ G+ 
Sbjct: 69  SSLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVA 128

Query: 121 VGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLF 180
           VG A+   P YIAE++PA+ RG+L +LQ+L IVSG  +A +SN     + GG        
Sbjct: 129 VGGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGE------- 181

Query: 181 GAAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRIEE 240
             + WRWM     +PA+L       +P+SPR+   +G+  +A  +L +    D     E 
Sbjct: 182 --STWRWMLAVATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHKD-DVEWEL 238

Query: 241 IQATVSLDH-----KPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRS 295
           ++ T +LD      KPRFS++++    L  +  IG+G++ +QQ  G+N I YY+  +  S
Sbjct: 239 LEITETLDEQRNLGKPRFSEIMT--PWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTS 296

Query: 296 VGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVV-FGG 354
           VG T+  +L  T+  G +++L T V I  + K GR+P+ ++G  G T  L  +  V +  
Sbjct: 297 VGMTDNAALFATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLL 356

Query: 355 ATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWG---PIVWVLLGEMFNNKIRAAALSVA 411
              VNGQP    A     +V A + +F   F  G   P+ W+L+ E+F  ++R   +  A
Sbjct: 357 PETVNGQPDALRA----YMVLAGMLLF-LSFQQGALSPVTWLLMSEIFPTRLRGIFMGGA 411

Query: 412 AGVQWIANFIISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
               WIANF+IS  FP LL  +GL   + ++A        F+   V ET+ ++LEQ+
Sbjct: 412 VFSMWIANFLISLFFPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQI 468


Lambda     K      H
   0.325    0.140    0.430 

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: 638
Number of extensions: 41
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: 468
Length of database: 499
Length adjustment: 34
Effective length of query: 434
Effective length of database: 465
Effective search space:   201810
Effective search space used:   201810
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 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