GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Burkholderia phytofirmans PsJN

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BPHYT_RS04440 BPHYT_RS04440 ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__BFirm:BPHYT_RS04440
          Length = 291

 Score =  140 bits (352), Expect = 5e-38
 Identities = 94/304 (30%), Positives = 158/304 (51%), Gaps = 16/304 (5%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60
           M   LQ + +G++LG IY +IA GY + +   G +NF  G+  M+GA V L     + +L
Sbjct: 1   MAILLQLIYSGIALGMIYAVIAFGYQLTFATSGTLNFGQGDALMLGALVGL----TLVTL 56

Query: 61  GITWVPLALLVMLVASMLFTAVYGWTVERIAYRP-LRSSPRLAPLISAIGMSIFLQNYVQ 119
           G+ +    L++ LV   +F  + G  VERI  RP +R       ++S I + I  +N  +
Sbjct: 57  GVNYW---LMIPLVC--VFGLLQGAFVERIGVRPAIRIKSEFGWIMSTIALGIIFKNVAE 111

Query: 120 ILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179
            L G         LP     + GA +V  + L  +   + +M        +T  G+A  A
Sbjct: 112 NLWGRDDLRFPSPLPEAPLKVFGA-NVLPMELLVVGGALVMMLAVEFFNRKTIFGKAVVA 170

Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMV--LLIYGVIDFYIGFLAGVKAFT 237
              D+  A L+G+N   VI+ ++ + +  AA AG+++  L + G     +G + G+KAF 
Sbjct: 171 TANDRDAAALMGINTGLVITFSYALSSLTAAFAGVLIAPLTLTGAT---MGAVLGLKAFA 227

Query: 238 AAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPE 297
            A++GG+ S  G ++GGV++G+ E     Y+ + +KDV    +L++VL  +P GL G+  
Sbjct: 228 VAIIGGLSSGLGIVVGGVILGIAETTTGFYISTGYKDVPGLVLLLIVLALKPAGLFGKTS 287

Query: 298 IEKV 301
           I+KV
Sbjct: 288 IKKV 291


Lambda     K      H
   0.329    0.144    0.425 

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: 317
Number of extensions: 24
Number of successful extensions: 4
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: 301
Length of database: 291
Length adjustment: 26
Effective length of query: 275
Effective length of database: 265
Effective search space:    72875
Effective search space used:    72875
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: 48 (23.1 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