GapMind for catabolism of small carbon sources

 

Alignments for a candidate for exuT in Klebsiella michiganensis M5al

Align Hexuronate transporter (characterized)
to candidate BWI76_RS24735 BWI76_RS24735 MFS transporter

Query= SwissProt::P0AA78
         (432 letters)



>FitnessBrowser__Koxy:BWI76_RS24735
          Length = 433

 Score =  780 bits (2014), Expect = 0.0
 Identities = 382/417 (91%), Positives = 403/417 (96%)

Query: 1   MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60
           MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEEL+ISTQQYSYIIAAYSAAYTV
Sbjct: 1   MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELHISTQQYSYIIAAYSAAYTV 60

Query: 61  MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120
           MQPVAGYVLDVLGTKIGYA FA+ WAVFCG+TALAGSWGGLA+ARGAVGAAEAAMIPAGL
Sbjct: 61  MQPVAGYVLDVLGTKIGYAFFAIAWAVFCGSTALAGSWGGLALARGAVGAAEAAMIPAGL 120

Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180
           KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISG LSF WAMA
Sbjct: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGVLSFAWAMA 180

Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAE 240
           WL+FYKHPRDQK LT+EER+YII GQE+ HQ +  KKMS  QILRNRQFWGIALPRFLAE
Sbjct: 181 WLVFYKHPRDQKKLTEEERNYIIGGQESHHQTNNGKKMSPWQILRNRQFWGIALPRFLAE 240

Query: 241 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIV 300
           PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCI+GGYLPPLFQRWFGVNLIV
Sbjct: 241 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCIVGGYLPPLFQRWFGVNLIV 300

Query: 301 SRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVA 360
           SRKMVVT+GA+LMIGPGMIGLFT+P+VAI LLC+GGFAHQALSGALITLSSDVFGRNEVA
Sbjct: 301 SRKMVVTMGALLMIGPGMIGLFTSPFVAIALLCVGGFAHQALSGALITLSSDVFGRNEVA 360

Query: 361 TANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNKPA 417
           TANG+TGM+AWLAST+FALVVGALADTIGFSPLFAVLAVFD+LGA+VIWTVL+NK A
Sbjct: 361 TANGMTGMAAWLASTMFALVVGALADTIGFSPLFAVLAVFDVLGAVVIWTVLKNKSA 417


Lambda     K      H
   0.326    0.138    0.437 

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: 871
Number of extensions: 25
Number of successful extensions: 1
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: 432
Length of database: 433
Length adjustment: 32
Effective length of query: 400
Effective length of database: 401
Effective search space:   160400
Effective search space used:   160400
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:

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