GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Klebsiella michiganensis M5al

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter

Query= SwissProt::P11551
         (438 letters)



>FitnessBrowser__Koxy:BWI76_RS23685
          Length = 444

 Score =  298 bits (763), Expect = 2e-85
 Identities = 166/407 (40%), Positives = 240/407 (58%), Gaps = 6/407 (1%)

Query: 26  IPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILM 85
           + F L+C LF LW +A NLNDIL+ QF++ F LT+ Q  L+QS F+ GYF + +PA  L+
Sbjct: 31  LQFLLVCCLFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVALPAAALI 90

Query: 86  KKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVL 145
           K+ SYKA II GL LYALG  LF PAA+IM Y  FL  L +IA GL  LET+AN + ++L
Sbjct: 91  KRYSYKAAIIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSANTYSSLL 150

Query: 146 GPESSGHFRLNLAQTFNSFGAIIAVVFGQSLIL-SNVPHQSQDVLDKMSPEQLSAYKHSL 204
           GP  S   R+N +Q FNS G I  V+ GQ ++   N P  S + L  M      A +H +
Sbjct: 151 GPIQSSTQRINFSQIFNSLGVISGVLIGQVMVFGENDP--SHEQLLAMPAAAADAARHQM 208

Query: 205 VLSVQTPYMIIVAIVLLVALLIMLTKFPALQS--DNHSDAKQGSFSASLSRLARIRHWRW 262
           V  V  PY+II ++++++AL+ +  KFP+ +            S  ++L RL  I  +R 
Sbjct: 209 VGQVVGPYLIIGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAIPRFRL 268

Query: 263 AVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISRF 322
            +L+QF YVGAQ   WS+ IR+      G +   A  +L  ++V + +G+   TWL++R 
Sbjct: 269 GILSQFLYVGAQVGVWSFTIRFVQLVQQGTSEHSATYWLLASLVIYAVGKTVATWLMNRL 328

Query: 323 APHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKY 382
            P  +L  +AL A  L LI+ F+   + + AL L S  M+  +PT F L IK +G+DT+ 
Sbjct: 329 NPALLLGTFALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMGKDTQT 388

Query: 383 GSSFIVMTIIGGGIVTPVMGFVSDA-AGNIPTAELIPALCFAVIFIF 428
             S +VM+IIGG ++  VMG +SD   GN+  A + P LCF  +  +
Sbjct: 389 AGSIVVMSIIGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFY 435


Lambda     K      H
   0.329    0.140    0.425 

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: 481
Number of extensions: 24
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 438
Length of database: 444
Length adjustment: 32
Effective length of query: 406
Effective length of database: 412
Effective search space:   167272
Effective search space used:   167272
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 (21.8 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