GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Herbaspirillum seropedicae SmR1

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate HSERO_RS21250 HSERO_RS21250 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__HerbieS:HSERO_RS21250
          Length = 244

 Score =  262 bits (670), Expect = 4e-75
 Identities = 136/246 (55%), Positives = 178/246 (72%), Gaps = 3/246 (1%)

Query: 7   PLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66
           PLI+ D ++K FG  +VL+G++ ++ P +VI+IIG SG GKST LRC+N LE I  G + 
Sbjct: 2   PLIAIDNVKKRFGDNEVLKGISLDVEPGEVIAIIGKSGSGKSTLLRCINGLESIDEGNIS 61

Query: 67  VAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDR 126
           VAG  L  ++++   LR LR++VGM+FQ FNLFPHL+V +N+++AP  V  +  AEA   
Sbjct: 62  VAGAKLGASELE---LRNLRLKVGMIFQQFNLFPHLSVGRNVMIAPMIVKGVSEAEAMKT 118

Query: 127 ALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVL 186
           A   L+KVGLG K D YPDQLSGGQ+QRVAIAR L M P+ LL DE TSALDPELV EVL
Sbjct: 119 AKANLEKVGLGHKFDAYPDQLSGGQQQRVAIARALSMSPQALLCDEITSALDPELVNEVL 178

Query: 187 NVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246
            VM+ LA+EGMT+ +VTHEM+FAREV NR+ F +QG + E G P E+F NPK+  L+ F+
Sbjct: 179 TVMRGLAKEGMTLLMVTHEMRFAREVCNRLVFMHQGKVHEIGPPEELFGNPKTPELQQFI 238

Query: 247 SRIQSS 252
              Q +
Sbjct: 239 GMTQGA 244


Lambda     K      H
   0.321    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: 211
Number of extensions: 8
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: 252
Length of database: 244
Length adjustment: 24
Effective length of query: 228
Effective length of database: 220
Effective search space:    50160
Effective search space used:    50160
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: 46 (22.3 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