GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Klebsiella michiganensis M5al

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BWI76_RS05985 BWI76_RS05985 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Koxy:BWI76_RS05985
          Length = 349

 Score =  145 bits (366), Expect = 2e-39
 Identities = 110/341 (32%), Positives = 167/341 (48%), Gaps = 27/341 (7%)

Query: 7   NWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66
           N +I  + + +L  I   F +  +R+     ++++LA+  N++ G  G L L    F AV
Sbjct: 14  NLVIIVLCVALLAGINVVFNDYIIRVISTIFVFMILAVSYNLINGVTGQLSLEPNGFVAV 73

Query: 67  GAYLFALM--ASPHLADNFAAFA-AMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123
           GAY+ AL+  +S    D F   A + +   LH      + ++ L AA     L  P  ++
Sbjct: 74  GAYVTALLILSSDSKLDMFEMAAPSPWILVLHAGFLPALLISGLCAAALAVCLALPVFRV 133

Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI 183
           RGDYLAIVTLGFG II+I   N  +P  +TNG  GL  I                     
Sbjct: 134 RGDYLAIVTLGFGFIIKILAIN--NP-QITNGAIGLNDIPQ------------------- 171

Query: 184 NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGM 243
               L++     L+   +I+  +L  S+ GR   A+R+DE AA AMG+NT  +K  AF  
Sbjct: 172 QPHLLFWCGLFALLATGMIL--QLVWSKYGRMMKAVRDDEDAAIAMGVNTFRIKTCAFAT 229

Query: 244 GASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEV 303
            A F G+ G +  +    +SP  F  M +  ++ ++VLGG+G   G +LG VL+    E 
Sbjct: 230 SAFFEGIGGGLLASLLTTISPGLFDFMLTFQLLIIIVLGGLGSTTGALLGTVLVVGSGEW 289

Query: 304 LRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
           LR++  PLQ           LR ++ +L ++IIML    GL
Sbjct: 290 LRFLDQPLQFFGHDLGAYPGLRMVVFSLLLLIIMLFAREGL 330


Lambda     K      H
   0.328    0.144    0.430 

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: 293
Number of extensions: 13
Number of successful extensions: 3
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: 358
Length of database: 349
Length adjustment: 29
Effective length of query: 329
Effective length of database: 320
Effective search space:   105280
Effective search space used:   105280
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