GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02872 in Klebsiella michiganensis M5al

Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease

Query= reanno::Smeli:SMc02872
         (315 letters)



>FitnessBrowser__Koxy:BWI76_RS03135
          Length = 290

 Score =  114 bits (286), Expect = 2e-30
 Identities = 78/256 (30%), Positives = 124/256 (48%), Gaps = 24/256 (9%)

Query: 17  RRWHILVFLLPALVVYTAVMILPLFETLRQSFYNT--VDGQLTFVGLGNFKVLFGDPRWA 74
           + W   + L P+L+        PL  ++  S ++T  V     +VGL NF  LF D    
Sbjct: 3   KTWLPWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFAD---- 58

Query: 75  ADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKL---RFGAFYRTAIFLPTLLSFVI 131
           + FW +L NN ++ L+ +      G+ LA +L+V      R   + RTA F P ++  V 
Sbjct: 59  SVFWQSLVNNLLYILLTVVP----GVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVS 114

Query: 132 VGFIWKLILSPIWGVAPYLLDTVGLRSLFGP----WLGKPDTALIAVSLISVWQYIGIPM 187
              +W  I  P  G+  + L       LFGP    WLG+ ++AL+A++LI VW++ G  M
Sbjct: 115 AAALWLFIFMPGLGLLDHYL-----AKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYM 169

Query: 188 MLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNAFDLIY 247
           +   A L +IP    EAA ++G T    F+K+ LPL+ P +  V     + +    D + 
Sbjct: 170 LFFLAGLQSIPASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVA 229

Query: 248 TVQGALAGPDKSTDIL 263
            +     GPD +T +L
Sbjct: 230 VM--TRGGPDNATTVL 243


Lambda     K      H
   0.331    0.146    0.461 

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: 278
Number of extensions: 15
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: 315
Length of database: 290
Length adjustment: 27
Effective length of query: 288
Effective length of database: 263
Effective search space:    75744
Effective search space used:    75744
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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