GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Phaeobacter inhibens BS107

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF3910 PGA1_65p00130 putative amino-acid ABC transporter, ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__Phaeo:GFF3910
          Length = 251

 Score =  205 bits (521), Expect = 9e-58
 Identities = 111/242 (45%), Positives = 155/242 (64%), Gaps = 3/242 (1%)

Query: 22  AIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIV 81
           AI I+ + K +G   VL  I+LT+  GERIVI GPSG+GKST++RC+N L+   +G + +
Sbjct: 9   AISITGLRKTFGDSVVLDGIDLTIQPGERIVIIGPSGTGKSTLLRCLNFLDAPDAGLVRI 68

Query: 82  DGIELTS---DLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETA 138
             +++ +       I  +R     VFQ++ LF + T  EN+  A I V+K P+ EAE  A
Sbjct: 69  GDLDVDAARASKAEILALRRRTAFVFQNYALFANKTAAENIMEALITVQKQPRAEAEARA 128

Query: 139 MYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLD 198
              L +  + ++A  YP  LSGGQQQRV I R++ +  ++MLFDEPTSALDPE + EVL 
Sbjct: 129 REILAETGLADKADAYPASLSGGQQQRVGIGRAMALGAELMLFDEPTSALDPEWVGEVLA 188

Query: 199 TMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLS 258
            M ++AEE  TML VTHEM FA+ +A+RV+FM  G+IVEQ  P   F  PQ  RT+ FL 
Sbjct: 189 LMHKVAEERQTMLIVTHEMQFAREIADRVVFMEGGRIVEQGPPTQIFDAPQDPRTRAFLR 248

Query: 259 QI 260
           ++
Sbjct: 249 RV 250


Lambda     K      H
   0.320    0.134    0.391 

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: 141
Number of extensions: 5
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: 263
Length of database: 251
Length adjustment: 24
Effective length of query: 239
Effective length of database: 227
Effective search space:    54253
Effective search space used:    54253
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 (21.8 bits)
S2: 47 (22.7 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