GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Klebsiella michiganensis M5al

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= SwissProt::P37772
         (331 letters)



>FitnessBrowser__Koxy:BWI76_RS14865
          Length = 339

 Score =  169 bits (429), Expect = 7e-47
 Identities = 112/303 (36%), Positives = 173/303 (57%), Gaps = 15/303 (4%)

Query: 10  ITIGVFVLGYLYCLTQF-PGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSV 68
           + I + +L  L  ++ F P F     + NI    +   I+A GMTFVIL+ GIDLSVGS+
Sbjct: 25  VGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSI 84

Query: 69  IAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLR 128
           +A +GV ++ V    G+   LA    + +G   G   G+L   L +  FI+TL  M FLR
Sbjct: 85  VAVSGV-VSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLR 143

Query: 129 GVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGL---LMLAVVVIGIFLAHRTRF 185
           G++Y ++E       PI    SSL+++  G G L  + +   +ML V ++  F+  RTRF
Sbjct: 144 GMAYTITE-----GQPIVS--SSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTRF 196

Query: 186 GNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVEL 245
           G  +YA+GGNA +A L G+  +     +YM++   A LAGI+F+    +    AG G EL
Sbjct: 197 GRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYEL 256

Query: 246 DAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAI-GILLFIF 304
           DAIA+VV+GGT L+GG G ++GTL G  I G++ T +        ++T++ I GI++ + 
Sbjct: 257 DAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSV--PFFTQLLIKGIVIILA 314

Query: 305 IAL 307
           +A+
Sbjct: 315 VAI 317


Lambda     K      H
   0.329    0.145    0.428 

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: 344
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: 331
Length of database: 339
Length adjustment: 28
Effective length of query: 303
Effective length of database: 311
Effective search space:    94233
Effective search space used:    94233
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: 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