Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BPHYT_RS04440 BPHYT_RS04440 ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__BFirm:BPHYT_RS04440 Length = 291 Score = 140 bits (352), Expect = 5e-38 Identities = 94/304 (30%), Positives = 158/304 (51%), Gaps = 16/304 (5%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M LQ + +G++LG IY +IA GY + + G +NF G+ M+GA V L + +L Sbjct: 1 MAILLQLIYSGIALGMIYAVIAFGYQLTFATSGTLNFGQGDALMLGALVGL----TLVTL 56 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRP-LRSSPRLAPLISAIGMSIFLQNYVQ 119 G+ + L++ LV +F + G VERI RP +R ++S I + I +N + Sbjct: 57 GVNYW---LMIPLVC--VFGLLQGAFVERIGVRPAIRIKSEFGWIMSTIALGIIFKNVAE 111 Query: 120 ILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179 L G LP + GA +V + L + + +M +T G+A A Sbjct: 112 NLWGRDDLRFPSPLPEAPLKVFGA-NVLPMELLVVGGALVMMLAVEFFNRKTIFGKAVVA 170 Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMV--LLIYGVIDFYIGFLAGVKAFT 237 D+ A L+G+N VI+ ++ + + AA AG+++ L + G +G + G+KAF Sbjct: 171 TANDRDAAALMGINTGLVITFSYALSSLTAAFAGVLIAPLTLTGAT---MGAVLGLKAFA 227 Query: 238 AAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPE 297 A++GG+ S G ++GGV++G+ E Y+ + +KDV +L++VL +P GL G+ Sbjct: 228 VAIIGGLSSGLGIVVGGVILGIAETTTGFYISTGYKDVPGLVLLLIVLALKPAGLFGKTS 287 Query: 298 IEKV 301 I+KV Sbjct: 288 IKKV 291 Lambda K H 0.329 0.144 0.425 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: 317 Number of extensions: 24 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: 301 Length of database: 291 Length adjustment: 26 Effective length of query: 275 Effective length of database: 265 Effective search space: 72875 Effective search space used: 72875 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: 48 (23.1 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