Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate BPHYT_RS34465 BPHYT_RS34465 glutamate/aspartate ABC transporter permease GltJ
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__BFirm:BPHYT_RS34465 Length = 245 Score = 261 bits (667), Expect = 9e-75 Identities = 128/245 (52%), Positives = 177/245 (72%), Gaps = 2/245 (0%) Query: 1 MSIDWNWGIFLQQAPFG-NTTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNR 59 M W+WG+ LQ G +TTYLGW++SG T+ L++ A+ +A +VG+ FGILRT+P+R Sbjct: 1 MDYSWDWGVLLQVVSTGEHTTYLGWLFSGLLNTVLLTVSAYALALVVGTGFGILRTLPSR 60 Query: 60 FLSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLG 119 S LGT YV +FR VPLIVQFF W+ V+PEL+P ++G WFK L P QF S+ LG Sbjct: 61 PASMLGTAYVSVFRGVPLIVQFFIWFFVVPELVPTELGDWFK-NLPPYTQFLSVSIFSLG 119 Query: 120 LFTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNL 179 ++T +R+CEQVRA IQ+LPRGQ +A A+GLT Q YRYVLLP +R I+ P+TSE + + Sbjct: 120 IYTGSRICEQVRAGIQALPRGQFDAGFALGLTRAQTYRYVLLPVTFRTILGPLTSEFLII 179 Query: 180 VKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRL 239 KNSA+ASTIGL++++ QA +L+DY+A +ESF +TLAY+ +N I+ M + R+ RL Sbjct: 180 SKNSAVASTIGLLELSGQARQLVDYTAQPYESFICVTLAYMALNFAILHGMNWIRRQTRL 239 Query: 240 PGNMG 244 PG +G Sbjct: 240 PGLLG 244 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: 239 Number of extensions: 12 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: 245 Length adjustment: 24 Effective length of query: 222 Effective length of database: 221 Effective search space: 49062 Effective search space used: 49062 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.
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:
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