GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Klebsiella michiganensis M5al

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__Koxy:BWI76_RS14865
          Length = 339

 Score =  241 bits (615), Expect = 2e-68
 Identities = 140/301 (46%), Positives = 202/301 (67%), Gaps = 10/301 (3%)

Query: 43  LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102
           L+L+IL  +FA PNF  VDNL++I +S +VN +LA   T+VI+TSGIDLSVG+++    V
Sbjct: 32  LVLLILMSTFA-PNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSIVAVSGV 90

Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162
           ++ VV    G+P PL I A +  GAL G ++G++ A L + PFI TLG M  L+G++  I
Sbjct: 91  VS-VVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRGMAYTI 149

Query: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTF 222
           +  +PI  + +  F  +    LIG     +PIP  V+I+ +V + A  IL +T FGR+ +
Sbjct: 150 TEGQPIV-SSSLSFRELGNGYLIG-----IPIP--VIIMLVVYLLAWFILERTRFGRHIY 201

Query: 223 ALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAA 282
           A+G N +A RL+GV+V     AVY  +G   G+AG+I A+R+ SAQP  G GYELDAIAA
Sbjct: 202 AVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYELDAIAA 261

Query: 283 VVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILR 342
           VV+GGTSL+GG G I+GT+IG+ I+ VL  GL ++SV    Q ++ G++IILAV +D L+
Sbjct: 262 VVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILAVAIDGLK 321

Query: 343 R 343
           +
Sbjct: 322 Q 322


Lambda     K      H
   0.326    0.139    0.398 

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: 308
Number of extensions: 15
Number of successful extensions: 3
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: 347
Length of database: 339
Length adjustment: 29
Effective length of query: 318
Effective length of database: 310
Effective search space:    98580
Effective search space used:    98580
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