GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Burkholderia phytofirmans PsJN

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate BPHYT_RS11445 BPHYT_RS11445 putrescine/spermidine ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__BFirm:BPHYT_RS11445
          Length = 388

 Score =  160 bits (405), Expect = 4e-44
 Identities = 83/233 (35%), Positives = 143/233 (61%), Gaps = 6/233 (2%)

Query: 32  DILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNI 91
           D++ + G TV +  V+L +  G++F ++G SG GKSTL+R +  L   +SG++L DG+++
Sbjct: 35  DVVKKFGETVAVKGVNLSVKKGELFALLGSSGCGKSTLLRMMAGLESVSSGKILIDGEDL 94

Query: 92  LDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTV 151
             L          R V+M+FQS+AL PH TV  NV +G +  GV K + ++     ++ V
Sbjct: 95  AQLPPYR------RPVNMMFQSYALFPHMTVEGNVAFGLKQEGVPKAELKDRVQTALELV 148

Query: 152 GLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQR 211
            +  +  + P+QLSGG +QRV LAR+L     ++L+DE  SALD  IR   Q +L+ +  
Sbjct: 149 QMGRFAKRKPNQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKQIRQRTQIELVNILD 208

Query: 212 NLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
            +  T + +THD +EA+ +   +A++ +G++VQ+GTP+++ + P + + A F+
Sbjct: 209 KVGVTCMMVTHDQEEAMTMAGRLAVMSEGEIVQLGTPHEVYEYPNSRFSAEFI 261


Lambda     K      H
   0.323    0.139    0.397 

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: 233
Number of extensions: 7
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: 275
Length of database: 388
Length adjustment: 28
Effective length of query: 247
Effective length of database: 360
Effective search space:    88920
Effective search space used:    88920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 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