GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Burkholderia phytofirmans PsJN

Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate BPHYT_RS27975 BPHYT_RS27975 ABC transporter permease

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__BFirm:BPHYT_RS27975
          Length = 318

 Score =  180 bits (456), Expect = 4e-50
 Identities = 94/284 (33%), Positives = 164/284 (57%), Gaps = 6/284 (2%)

Query: 9   LAWILVLPTLLVVVLVAGYPLAQVFYWSF--FKADIAFVEPPEFVGLENYAYLFQDPDFR 66
           +AW+ +LPT+L+++ +  +PL      SF  FK+++  V P  FVG++NY  +  D D  
Sbjct: 32  IAWLFILPTVLLLLAINIFPLIWALRLSFTNFKSNMPSV-PARFVGIDNYVDILTDEDIW 90

Query: 67  QALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWM 126
            A+  T +F   SV LE +LG  +AL+I+  FRG     T IL+P  +   V    W ++
Sbjct: 91  YAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILLPMMLSPAVVGNFWTFL 150

Query: 127 LNDVYGVIN-VLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIP 185
           L    G+ N ++G   G+       +    L   +I+ VD W  TP++ L+ LAGL+ IP
Sbjct: 151 LQPQTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMWTPYVMLICLAGLRSIP 210

Query: 186 EELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--AT 243
           + +YEAA +D A+ W+QFWSITLP+  P L++A++FR ++  ++FD+V +++   P   T
Sbjct: 211 DYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKMFDMVNLLTSGGPGSVT 270

Query: 244 RTLAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287
            T+++  ++   +    GY SA+++ + V +F    +Y++ + +
Sbjct: 271 ETVSITLKRAAFEKWQTGYSSALAIILFVTVFGAANIYVKALNR 314


Lambda     K      H
   0.329    0.142    0.433 

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: 276
Number of extensions: 13
Number of successful extensions: 3
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: 291
Length of database: 318
Length adjustment: 27
Effective length of query: 264
Effective length of database: 291
Effective search space:    76824
Effective search space used:    76824
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: 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