GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate H281DRAFT_00383 H281DRAFT_00383 amino acid ABC transporter membrane protein, PAAT family

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>FitnessBrowser__Burk376:H281DRAFT_00383
          Length = 225

 Score =  159 bits (403), Expect = 3e-44
 Identities = 88/211 (41%), Positives = 128/211 (60%), Gaps = 3/211 (1%)

Query: 13  PQLLAGALVTVEITAASLLLGCVMGLLVGIGRL-NPKRRVVYALCTAYVAAIRGTPLLVQ 71
           P L AG + TV +T AS  +G  +  +V + RL  PK  V  A+   YV   RG+PLLVQ
Sbjct: 14  PLLYAGLVFTVPLTLASFAIGLALAFIVALVRLFGPKWAV--AVVRFYVWLFRGSPLLVQ 71

Query: 72  LFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSG 131
           LF++F+GLP  GI+L      +IG  +  GAY SEV+RG I+SI KGQ EAA S+GM+  
Sbjct: 72  LFVIFYGLPNVGIVLDPLTAAIIGFSLNVGAYNSEVIRGVIESIPKGQWEAAYSMGMTRE 131

Query: 132 LAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYL 191
            A+R  +LPQA    +PPL N FIAL+K+++L ++LT+ ++    Q+I SV+Y  L +Y 
Sbjct: 132 QALRRAILPQAARVALPPLSNSFIALVKDTSLAAVLTVPEVFQAAQRIASVTYEPLILYT 191

Query: 192 AIAVVYFILTGATTLVLRRIELRLRAGGMVQ 222
             A+VY + +   +    R+E +     + Q
Sbjct: 192 EAALVYLLFSSVLSSAQVRLERKFGRHALFQ 222


Lambda     K      H
   0.328    0.143    0.412 

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: 158
Number of extensions: 3
Number of successful extensions: 1
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: 222
Length of database: 225
Length adjustment: 22
Effective length of query: 200
Effective length of database: 203
Effective search space:    40600
Effective search space used:    40600
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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