GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Burkholderia phytofirmans PsJN

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate BPHYT_RS16695 BPHYT_RS16695 glutamate/aspartate ABC transporter permease GltJ

Query= SwissProt::P0AER3
         (246 letters)



>FitnessBrowser__BFirm:BPHYT_RS16695
          Length = 246

 Score =  329 bits (844), Expect = 3e-95
 Identities = 159/247 (64%), Positives = 197/247 (79%), Gaps = 2/247 (0%)

Query: 1   MSIDWNWGIFLQQAPFGN-TTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNR 59
           MS  WNWGI L     G  TTYLGW+ SGF VTI +S+ AW+IA +VGS FG+LRTVPN+
Sbjct: 1   MSYHWNWGILLSPVSTGEPTTYLGWLLSGFWVTITVSLSAWVIALIVGSLFGVLRTVPNK 60

Query: 60  FLSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLG 119
           + SG+GTLYV +FRN+PLIVQFF WYLVIPELLP  +G WFK +L P  QFF SS++CLG
Sbjct: 61  WASGIGTLYVAIFRNIPLIVQFFIWYLVIPELLPASMGNWFK-QLPPGAQFFSSSIICLG 119

Query: 120 LFTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNL 179
           LFTAARVCEQVR+ I +LP+GQ+ A LAMG T  Q YRYVLLP AYR+IVPP+TSE +N+
Sbjct: 120 LFTAARVCEQVRSGINALPKGQRAAGLAMGFTQWQTYRYVLLPVAYRIIVPPLTSEFLNI 179

Query: 180 VKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRL 239
            KNSA+ASTIGL+D++AQA +L+DY++  +ESF A+T+AY+LIN  +M +M  VE K RL
Sbjct: 180 FKNSAVASTIGLLDLSAQARQLVDYTSQTYESFIAVTIAYMLINLVVMQLMRWVEAKTRL 239

Query: 240 PGNMGGK 246
           PG +GGK
Sbjct: 240 PGYIGGK 246


Lambda     K      H
   0.328    0.140    0.443 

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: 280
Number of extensions: 5
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: 246
Length of database: 246
Length adjustment: 24
Effective length of query: 222
Effective length of database: 222
Effective search space:    49284
Effective search space used:    49284
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: 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