GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Burkholderia phytofirmans PsJN

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>FitnessBrowser__BFirm:BPHYT_RS21680
          Length = 476

 Score =  300 bits (768), Expect = 7e-86
 Identities = 170/452 (37%), Positives = 244/452 (53%), Gaps = 16/452 (3%)

Query: 1   MDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFM 60
           M  +     LK GLK RH+ +IALGG IG GLF+GS  V+Q AGP+ +L + I G +  +
Sbjct: 1   MQRSTDTTELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVL 60

Query: 61  IMRQLGEMVAQEPVAGSFSHFAYKYWG------DFPGFLSGWNYWVLYVLVSMAELTAVG 114
           +MR LGEM    P  GSF  +A   +G      +  GFL+GW YW  +V+V   E  A  
Sbjct: 61  VMRMLGEMACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGA 120

Query: 115 TYVHYWWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLL 174
             V +W P VP W  +LV    + A NL +V +YGE EFWFA IKV A++  +  GG  +
Sbjct: 121 KLVQFWLPDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYV 180

Query: 175 VSGHGGPQ---ASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQK 231
           +      +   A +  L SHGG  P G   + +        + G E++ I AAEA EP K
Sbjct: 181 LGLWPAAKHVTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAK 240

Query: 232 SIPKAVNQVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVV 291
           ++ KA N VI R+L+FY+ S+ ++++L PWN      +P+V     +G    A+V+N +V
Sbjct: 241 AVAKATNSVITRVLVFYVGSILLVVALVPWNSPKMA-TPYVSALDAMGIPAAASVMNAIV 299

Query: 292 LTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNY 351
           LTA LS  NSG+YA SRM++ L   G+AP AL KV+RRGVP  AI +  +  +  V+++Y
Sbjct: 300 LTAVLSALNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSY 359

Query: 352 LIPAEALGLLMALVVAALVLNWALISLTHLKSR-RAMVAAGETLVFKSFWFPVSNWICLA 410
           + P      L+       +  + LI+++ LK R R    A E L  + + +P   W+ + 
Sbjct: 360 VSPDTVFAFLVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAII 419

Query: 411 FMALILVILAMTPGLSVSVLLVPLWLVVMWAG 442
            M  ILV +A  P         PLW  V   G
Sbjct: 420 GMVGILVAMAFIPEQR-----QPLWFGVASLG 446


Lambda     K      H
   0.327    0.140    0.440 

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: 535
Number of extensions: 33
Number of successful extensions: 6
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: 461
Length of database: 476
Length adjustment: 33
Effective length of query: 428
Effective length of database: 443
Effective search space:   189604
Effective search space used:   189604
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: 51 (24.3 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