Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_01522 H281DRAFT_01522 amino acid ABC transporter substrate-binding protein, PAAT family
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Burk376:H281DRAFT_01522 Length = 260 Score = 249 bits (635), Expect = 5e-71 Identities = 120/256 (46%), Positives = 171/256 (66%), Gaps = 5/256 (1%) Query: 6 LLGALALSVLSLPTFA----DEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEM 61 LL AL +++L+ + D ++ G++A+YPPF SK DG +VGFD D+GN +C + Sbjct: 4 LLAALTVALLATVSIGAHAKDWSTIRFGVDASYPPFESKGSDGKLVGFDIDLGNEICARL 63 Query: 62 KVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTA 121 K KCVWVE +FDG+IPALK +K D +LSSMS+T R + V F++K +NTP RLV K G+ Sbjct: 64 KAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQVAFSSKLFNTPTRLVAKKGSG 123 Query: 122 VSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVAD 181 + LKGK +GV++G+I E +A+ P GA++ PY +Q+++Y D+ +GRLD + D Sbjct: 124 ILPTAESLKGKTVGVEQGTIQETYAKTYWEPKGAKVVPYQNQDQVYADLLSGRLDAALQD 183 Query: 182 ATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAAIRENG 240 A + GFLKT G GF FVG D K G+G GI +RK D LK K++ AIA I ++G Sbjct: 184 AVQAEIGFLKTPRGAGFDFVGKNLDDPKILGNGAGIGMRKEDTDLKAKVDKAIADIIKDG 243 Query: 241 KYKQIQDKYFAFDIYG 256 YK+++ KYF FD+YG Sbjct: 244 TYKKLEKKYFDFDVYG 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