GapMind for catabolism of small carbon sources

 

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

Align 2-deoxy-D-ribonate transporter (characterized)
to candidate BPHYT_RS05360 BPHYT_RS05360 MFS transporter

Query= reanno::Burk376:H281DRAFT_00642
         (448 letters)



>FitnessBrowser__BFirm:BPHYT_RS05360
          Length = 439

 Score =  280 bits (715), Expect = 9e-80
 Identities = 151/403 (37%), Positives = 231/403 (57%), Gaps = 5/403 (1%)

Query: 19  RKAMARLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLEVP 78
           RK   RL PL+   Y +++LDR NV  AKLQ+ +D+G+S A YGFG+GIFF+GY + E+P
Sbjct: 26  RKVSWRLAPLLMLCYVVAYLDRVNVGFAKLQMTSDLGLSDAVYGFGAGIFFVGYFIFEIP 85

Query: 79  SNLAAHKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYMVT 138
           SN+  HKVG R WIARI V+WG++S   MFV   + FYV+R LLG+AEAG FP ++  +T
Sbjct: 86  SNVILHKVGARVWIARIMVSWGVISMLTMFVTTPTMFYVMRFLLGLAEAGFFPGIILYLT 145

Query: 139 LWFAPHDRPVVVGWIYIAPALALMLGNPLGGALMQ-LDGFGGLHGWQWMFMLEGIPSVIV 197
            W+  H R  +  W   A AL+ ++G P+ G +++  +G  G HGWQW+F+LEGIPSVIV
Sbjct: 146 YWYPAHRRGRMTTWFMTAIALSGVIGGPVSGYILKTFNGMNGWHGWQWLFLLEGIPSVIV 205

Query: 198 GIVLFFKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIGLI 257
           GI++F  + +R   A+WL+  E+ +LE H   +   + D         L     +++ L 
Sbjct: 206 GIMVFTMLDDRISKAKWLTKEEQQLLERHVSAEEATKHDMPIRQ---VLTSGRVLMLSLT 262

Query: 258 YFLNQVAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPR-IHRRTDRDC 316
           YF   +   G+ F+ P II    V  + ++G LSA    G ++ ++ + R   R+ +R  
Sbjct: 263 YFSFVMGLYGVSFWLPTIIKATGVTDAFMIGLLSAIPFAGAVVAMVFVSRSADRKRERRW 322

Query: 317 VFLGILTAGLILGACAYLAVTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGIQAAAG 376
                  AG +    + +   N    +A LT+        LP +W++    L G  AAAG
Sbjct: 323 HIALPAFAGAVGLVLSVVWAHNTVLAMASLTLATMGILTTLPLFWSLPTAILAGTGAAAG 382

Query: 377 LAFVNTIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVLG 419
           +A +N+IG + GF+ PY  G  + ++  +D+G  ++    VLG
Sbjct: 383 IAMINSIGNLAGFLSPYAVGWLKQATAANDSGMYMLAAFMVLG 425


Lambda     K      H
   0.329    0.142    0.436 

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: 592
Number of extensions: 30
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: 448
Length of database: 439
Length adjustment: 32
Effective length of query: 416
Effective length of database: 407
Effective search space:   169312
Effective search space used:   169312
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.

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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