GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Burkholderia phytofirmans PsJN

Align Sugar ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS29180 BPHYT_RS29180 sugar ABC transporter permease

Query= uniprot:A0A165KQ00
         (289 letters)



>FitnessBrowser__BFirm:BPHYT_RS29180
          Length = 306

 Score =  299 bits (766), Expect = 5e-86
 Identities = 143/277 (51%), Positives = 199/277 (71%)

Query: 13  RFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWSAWGTAWQSACTG 72
           R  VYA L  A  FFLLPLY MLVTS K   EIR  +LLA P     SAW  AWQSACTG
Sbjct: 30  RLGVYAFLLTAALFFLLPLYVMLVTSVKPMNEIRLGNLLAFPTHFTLSAWSAAWQSACTG 89

Query: 73  VDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFGMLLFGVFMPFQV 132
           +DCNG++  F NSV + VP+ ++S   GA+NGY LS W+ RG+  LFG+LL G F+P QV
Sbjct: 90  LDCNGIQVGFWNSVRIVVPSTILSIAIGAVNGYALSFWRPRGAGLLFGVLLMGAFIPVQV 149

Query: 133 VLLPMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELVNAARMDGASFF 192
           ++ P+ +VL  + L SS+ G+V++H + G+   TL FRNYY +IP+EL  AAR+DG  F+
Sbjct: 150 MVYPLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYYVSIPQELFKAARIDGGGFW 209

Query: 193 QIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVFSGTDSKPVTVGLNNLANTSSSVKA 252
           +IF +++LP+STPI++V +I Q T IWNDF+ G+VF+GT + P+TV LNN+ NT++  + 
Sbjct: 210 RIFVQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKNLPMTVQLNNIINTTTGERL 269

Query: 253 YNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTAGAVKG 289
           YNV+MAA I+  +  + +Y ++G++FVRG+ +GAVKG
Sbjct: 270 YNVNMAATILTSMVPLAVYFVSGRWFVRGIASGAVKG 306


Lambda     K      H
   0.327    0.139    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: 287
Number of extensions: 13
Number of successful extensions: 1
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: 289
Length of database: 306
Length adjustment: 26
Effective length of query: 263
Effective length of database: 280
Effective search space:    73640
Effective search space used:    73640
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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