Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate RR42_RS29660 RR42_RS29660 amino acid transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS29660 Length = 264 Score = 355 bits (910), Expect = e-103 Identities = 177/253 (69%), Positives = 211/253 (83%), Gaps = 1/253 (0%) Query: 3 KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 KL VQD+HK +G +EVLKGVSL A GDVISIIG+SGSGKSTFLRCIN LE+P +G+I L Sbjct: 12 KLAVQDIHKSFGDNEVLKGVSLTAKKGDVISIIGASGSGKSTFLRCINYLERPKSGQIFL 71 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + EE++ +K G L +PKQLQRMR++LSMVFQHFNLW+HM +ENI+EAP HVLG+S Sbjct: 72 DGEEIRTKKDKTGDLVVVEPKQLQRMRTKLSMVFQHFNLWAHMNVLENIIEAPTHVLGLS 131 Query: 123 KTEAREKAEHYLNKVGVAHR-KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALD 181 + EA E+A YL KVG+ R + YP H+SGG+QQRVAIARALAM P+VMLFDEPTSALD Sbjct: 132 RKEAEERAREYLEKVGLPPRVEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALD 191 Query: 182 PELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQ 241 PELVG+VLKVMQ LA+EGRTM+VVTHEMGFAR VSN ++FLH+G EE G P EVL +P+ Sbjct: 192 PELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEQGPPEEVLNSPR 251 Query: 242 SERLQQFLSGSLK 254 SERL+QFLSGSLK Sbjct: 252 SERLRQFLSGSLK 264 Lambda K H 0.317 0.131 0.366 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: 271 Number of extensions: 5 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: 254 Length of database: 264 Length adjustment: 24 Effective length of query: 230 Effective length of database: 240 Effective search space: 55200 Effective search space used: 55200 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