GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Acidovorax caeni R-24608

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_054254771.1 BN2503_RS00920 ABC transporter permease subunit

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>NCBI__GCF_001298675.1:WP_054254771.1
          Length = 237

 Score =  104 bits (260), Expect = 1e-27
 Identities = 74/213 (34%), Positives = 111/213 (52%), Gaps = 5/213 (2%)

Query: 25  QGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLLIFY 84
           QG  +T++L+  SL L  +L L  A A +S    LR PAQ +T  +RG P L+ + LI+Y
Sbjct: 17  QGLVVTLQLTLYSLGLGAVLALACALALVSPRVWLRWPAQTFTYFMRGTPLLIQVYLIYY 76

Query: 85  SLQT--WLTSLTDFMEWEYIEI-DPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAA 141
            +    W+ +  D + W + +  +PF   +++      AY  ET  G+I    +G+VEAA
Sbjct: 77  GVAQLEWVQARWDAV-WPWTQFKEPFFCTLLSFSLNTAAYTAETLAGSIRETNKGEVEAA 135

Query: 142 TAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSII-GLADLVKAAQDAGKS 200
            A G+  G   R +V P  +R  LP  GN  ++ML +++L S +  L DL  AA      
Sbjct: 136 RAMGMGHGMLMRRIVLPSAIRRMLPAYGNEVVMMLHSSSLASTVPALLDLTGAASRVYAD 195

Query: 201 TYQLFYFLVLAALIYLLITSASNFILRWLERRY 233
            +  F   + AA IYL IT A     + LERR+
Sbjct: 196 FFLPFEAYLFAAAIYLCITFALIGASKLLERRF 228


Lambda     K      H
   0.329    0.142    0.418 

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: 171
Number of extensions: 9
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: 242
Length of database: 237
Length adjustment: 23
Effective length of query: 219
Effective length of database: 214
Effective search space:    46866
Effective search space used:    46866
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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