GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Paraburkholderia bryophila 376MFSha3.1

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate H281DRAFT_02384 H281DRAFT_02384 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__Burk376:H281DRAFT_02384
          Length = 254

 Score =  199 bits (506), Expect = 4e-56
 Identities = 108/238 (45%), Positives = 156/238 (65%), Gaps = 7/238 (2%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRAR---MGR 57
           +L V+G+   YG +EAL G  I++ AG+IVS+IG NGAGKSTLL  I G+        G 
Sbjct: 11  ILDVNGLSVRYGKVEALHGAAIKVRAGQIVSVIGPNGAGKSTLLNAIMGALPTTGHAKGA 70

Query: 58  ITFEGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPG---SFANELE 114
           + ++G+D++ +P  + V  G+   PE R +F  MSV +NL +G+   K     +F +++E
Sbjct: 71  VVYQGEDVSAVPVEKRVARGMCLVPEKRELFASMSVEDNLVLGAYRRKRAGERNFLDQME 130

Query: 115 RVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQ 174
            V  LFPRLKER  Q AGT+SGGE+QMLA+GRALM +P LL+LDEPSLGLAPL+VK+IF 
Sbjct: 131 PVFQLFPRLKERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGLAPLIVKEIFH 190

Query: 175 AVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
            +  + R+  +   ++EQNA  AL+++  GYV+  G++ + G  ++L  N  V   YL
Sbjct: 191 IISAL-RQTGVATLLIEQNARAALQISDYGYVLETGELALEGAASDLAQNPRVIETYL 247


Lambda     K      H
   0.320    0.136    0.377 

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: 185
Number of extensions: 5
Number of successful extensions: 4
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: 236
Length of database: 254
Length adjustment: 24
Effective length of query: 212
Effective length of database: 230
Effective search space:    48760
Effective search space used:    48760
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: 46 (22.3 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