GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Burkholderia phytofirmans PsJN

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate BPHYT_RS20405 BPHYT_RS20405 MFS transporter

Query= reanno::WCS417:GFF1429
         (438 letters)



>FitnessBrowser__BFirm:BPHYT_RS20405
          Length = 443

 Score =  324 bits (831), Expect = 3e-93
 Identities = 170/404 (42%), Positives = 235/404 (58%), Gaps = 4/404 (0%)

Query: 21  LMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIMH 80
           ++PL +I +I +++DR NI     H+  DLGI AAAYGLG+GLFF+ YAL E+PSN++M 
Sbjct: 23  VLPLFLIMFIANYIDRVNIGFVNSHMQTDLGIGAAAYGLGSGLFFIGYALFEVPSNVLMQ 82

Query: 81  KVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNRE 140
           K GAR W+ RIM TWGL++AAMAFV  +TSFYVLR LLGIAEAG FPGV+ Y T W  ++
Sbjct: 83  KYGARAWLTRIMGTWGLVAAAMAFVWNDTSFYVLRFLLGIAEAGFFPGVVFYFTQWLPQK 142

Query: 141 QRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWRK 200
           +R +A   FL G   A+++ GP+  +L+ + G  G HGWQWMF++EG  ++    V W  
Sbjct: 143 ERGKAVAVFLGGSALASVLSGPITGSLLSIRG-FGLHGWQWMFLVEGGFSIVLCAVSWML 201

Query: 201 LPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGG---HSLKNWLTPQILLAIFVYFCHQ 257
           L  R   A WL+AEE   +E  IA E       GG    ++K    PQILL  F+YF  Q
Sbjct: 202 LKSRIRDASWLTAEEQHVLETSIAAEQAAREAHGGAHLPAMKLLKDPQILLFCFLYFAIQ 261

Query: 258 ITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTG 317
           +TIY   F+LP+II K G LS   VG+L ++PW+ A          +      +  L   
Sbjct: 262 LTIYAATFWLPTIIRKMGGLSDFQVGMLNAIPWLIAMFAMYCFALLSAKWRFQQAWLAVA 321

Query: 318 LLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNAC 377
           L+  A GL  ++   PV S +  C SA+ F    S+ +  P   L     A  +  +N+ 
Sbjct: 322 LVIAACGLFASTSGNPVLSFVAICFSAIGFKAAASLFWPIPQGYLDARVAAAVIALINSV 381

Query: 378 GLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLR 421
           G LGGF  P+  G ++Q TG+   GL  +A+  ++AA A    R
Sbjct: 382 GNLGGFFAPAAFGYLQQHTGSITGGLYGLAVASLIAAAAGFLTR 425


Lambda     K      H
   0.327    0.141    0.438 

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: 554
Number of extensions: 27
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: 438
Length of database: 443
Length adjustment: 32
Effective length of query: 406
Effective length of database: 411
Effective search space:   166866
Effective search space used:   166866
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