GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Burkholderia phytofirmans PsJN

Align histidine permease (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



>FitnessBrowser__BFirm:BPHYT_RS15500
          Length = 461

 Score =  389 bits (1000), Expect = e-113
 Identities = 195/458 (42%), Positives = 289/458 (63%), Gaps = 6/458 (1%)

Query: 6   NGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65
           +GLKRGL  RHI+ +ALG AIGTGLF GSAS +Q AGP+++L Y IGG   FM+MR LGE
Sbjct: 8   DGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQLGE 67

Query: 66  MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRW 125
           M    PVAGSF  +A  Y G   GF+ GW Y    V+V MA++TA G Y+ +W+P V  W
Sbjct: 68  MVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTW 127

Query: 126 IWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTD 185
           +  L   +++  +NL NVK +GE EFW +++KV A++ MI+ G G +L  IS   G    
Sbjct: 128 VSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFG-GYLL--ISGHGGPQAS 184

Query: 186 ISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRI 245
           I+NLW+ GGF P+G  GL    AV+MF+FGG+E+IG+TA EA  PQ  +P+A+N V  RI
Sbjct: 185 ITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRI 244

Query: 246 LLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIF 305
           L+FY+ ++ VL+S++PW ++ + GSPFV IF ++G +  A +LN+VV+TAA+S  NS ++
Sbjct: 245 LIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVY 304

Query: 306 GAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASI 365
              RM++GLA+QG+AP+    + R GVP+M + + ++A    V++NYLIP     L+ ++
Sbjct: 305 ANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMAL 364

Query: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFP 425
              A V  W +I  T +  R++M A     L F   ++P +    +AFM  +  +L   P
Sbjct: 365 VVAALVLNWALISLTHLKSRKAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILAMTP 423

Query: 426 DTQAALIVGVVWIVLLVLAYLMWVKPAA--GQAALVAR 461
               ++ +   W+V++   Y+   + AA  G A +V R
Sbjct: 424 GLSVSVWLVPAWLVVMWAGYVFKRRRAAVQGGARVVGR 461


Lambda     K      H
   0.329    0.142    0.441 

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: 684
Number of extensions: 34
Number of successful extensions: 2
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: 468
Length of database: 461
Length adjustment: 33
Effective length of query: 435
Effective length of database: 428
Effective search space:   186180
Effective search space used:   186180
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: 51 (24.3 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