GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Klebsiella michiganensis M5al

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__Koxy:BWI76_RS14865
          Length = 339

 Score =  204 bits (520), Expect = 2e-57
 Identities = 114/307 (37%), Positives = 184/307 (59%), Gaps = 9/307 (2%)

Query: 17  RWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLV 76
           +W   +  L+ LL++L++ S  AP+F +V         + ++I    +  A+LA GMT V
Sbjct: 20  KWWDRVGILIVLLVLLILMSTFAPNFNRV--------DNLLNIARSISVNAILAAGMTFV 71

Query: 77  IATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQP 136
           I T GIDLSVG+++A++G  +    +AG   P+ +L+ +G G L GL NG+L A L + P
Sbjct: 72  ILTSGIDLSVGSIVAVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAP 131

Query: 137 FVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLT 196
           F+ TL  M   RG+A  IT GQ +  +S      G+G L+ +P PVII ++  +L W + 
Sbjct: 132 FIVTLGTMTFLRGMAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFIL 191

Query: 197 RKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNA 256
            +T  G  I AVG N +AA+ AGV  + ++   Y+++G+CA +AGII AA +  A    A
Sbjct: 192 ERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQP-TA 250

Query: 257 GLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVV 316
           G   ELDAI AVV+GG SL GGR  ++ +++G++I+  ++TG++L   P     ++K +V
Sbjct: 251 GTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIV 310

Query: 317 VLCVLIV 323
           ++  + +
Sbjct: 311 IILAVAI 317


Lambda     K      H
   0.327    0.142    0.416 

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: 321
Number of extensions: 13
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: 341
Length of database: 339
Length adjustment: 28
Effective length of query: 313
Effective length of database: 311
Effective search space:    97343
Effective search space used:    97343
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: 49 (23.5 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