Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS29525 BPHYT_RS29525 ABC transporter substrate-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__BFirm:BPHYT_RS29525 Length = 260 Score = 250 bits (638), Expect = 2e-71 Identities = 123/261 (47%), Positives = 173/261 (66%), Gaps = 7/261 (2%) Query: 1 MKKLVLLGALALSVLSLPTFA----DEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNA 56 MKKL L AL +++L+ + D ++ G++A+YPPF SK DG +VGFD D+GN Sbjct: 1 MKKL--LAALTVALLATVSIGAHAKDWSTVRFGVDASYPPFESKGSDGKLVGFDIDLGNE 58 Query: 57 LCEEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVM 116 +C MK KCVWVE +FDG+IPALK +K D +LSSMS+T R + + F+NK +NTP RLV Sbjct: 59 ICARMKAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQIAFSNKLFNTPTRLVA 118 Query: 117 KAGTAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLD 176 K G+ + LKGK +GV++G+I E +A+ P G ++ PY +Q+++Y D+ +GRLD Sbjct: 119 KKGSGILPTADSLKGKTVGVEQGTIQETYAKTYWEPKGTKVVPYQNQDQVYADLLSGRLD 178 Query: 177 GTVADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAA 235 + DA + GFLKT G GF FVG D K G+G GI +RK D LK K++ AIA Sbjct: 179 AALQDAVQAEIGFLKTPRGAGFDFVGKNLDDPKILGNGAGIGMRKEDTDLKAKVDKAIAD 238 Query: 236 IRENGKYKQIQDKYFAFDIYG 256 I ++G YK+++ KYF FD+YG Sbjct: 239 IIKDGTYKKLEKKYFDFDVYG 259 Lambda K H 0.318 0.138 0.394 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: 236 Number of extensions: 6 Number of successful extensions: 2 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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