Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate H281DRAFT_03349 H281DRAFT_03349 amino acid ABC transporter membrane protein, PAAT family
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__Burk376:H281DRAFT_03349 Length = 222 Score = 120 bits (300), Expect = 3e-32 Identities = 76/222 (34%), Positives = 121/222 (54%), Gaps = 16/222 (7%) Query: 23 GW--IWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNR-FLSGLGTLYVELFRNVPLIV 79 GW I G VT+ ++ + ++ ++G GI R P R + G T Y+ FR PL+V Sbjct: 11 GWPDIMHGAIVTVEVTAASLALSCVLGLLIGIGRLTPQRRIVYGFCTAYLTFFRGTPLLV 70 Query: 80 QFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLGLFTAARVCEQVRAAIQSLPR 139 Q F + +P+ G+ A FL ML LGL++AA V E VR AIQS+ R Sbjct: 71 QLFLLFFGLPQF-----GILLPA--------FLCGMLGLGLYSAAYVSEIVRGAIQSVDR 117 Query: 140 GQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSAIASTIGLVDMAAQAG 199 GQ AA ++G++ QA R ++LP A ++PP+ +E + L+KNSA+ S + + D+ + Sbjct: 118 GQMEAARSIGMSSGQAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQ 177 Query: 200 KLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRLPG 241 K++ S + E + AI L Y+++ + VER++R G Sbjct: 178 KIISVSYRSLEVYLAIALVYLVLTQATNYALHRVERRLRAGG 219 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: 152 Number of extensions: 9 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: 222 Length adjustment: 23 Effective length of query: 223 Effective length of database: 199 Effective search space: 44377 Effective search space used: 44377 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