Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS21615 HSERO_RS21615 ABC transporter substrate-binding protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS21615 Length = 271 Score = 116 bits (290), Expect = 6e-31 Identities = 68/224 (30%), Positives = 115/224 (51%), Gaps = 5/224 (2%) Query: 28 IGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDAI 87 +G+E+AY PF+S+ +VGFD DI AL +++ ++ +V F+G L D + Sbjct: 51 VGVESAYAPFSSENEQKDVVGFDIDIMKALAKKIGIEVKFVPTPFEGFFNFLAQGDRDLL 110 Query: 88 LSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKKIGVQRGSIHNRFAE 147 +S+++ITD+RKKSV F+ Y+ + + A + +LK +G Q + + + Sbjct: 111 ISAITITDERKKSVAFSEPYFVATQTIALPAADTKVSKMEDLKPLTVGTQSATSGDELVQ 170 Query: 148 EVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDSGKGFAFVGPAFTD 207 +VL A+IK + S ++ +G +D VAD ++ + + K P+F Sbjct: 171 QVLGKNSAKIKRFDSTPLALKELESGGVDAVVADEPVVKNYIANNPNSKLRTVTDPSFPK 230 Query: 208 EKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQIQDKYF 251 E Y GIAVRK D L KIN + ++A+G + I +YF Sbjct: 231 EDY-----GIAVRKDDPELLAKINKGLAEMKADGSFAAISAQYF 269 Lambda K H 0.318 0.138 0.395 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: 189 Number of extensions: 10 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: 258 Length of database: 271 Length adjustment: 25 Effective length of query: 233 Effective length of database: 246 Effective search space: 57318 Effective search space used: 57318 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