Align Putative ABC transporter arginine-binding protein 2 (characterized)
to candidate RR42_RS34315 RR42_RS34315 ABC transporter substrate-binding protein
Query= SwissProt::P30859 (243 letters) >FitnessBrowser__Cup4G11:RR42_RS34315 Length = 254 Score = 102 bits (254), Expect = 7e-27 Identities = 79/245 (32%), Positives = 111/245 (45%), Gaps = 13/245 (5%) Query: 4 VLIAALIAGFSLSATAAETIRFATEASYPPFESIDAN-NQIVGFDVDLAQALCKEIDATC 62 +L AA F+ + AA T A+ PF +D N I G VD A+ K Sbjct: 13 ILCAASTVSFAWAQGAAPTYNVGATATGVPFTFLDVKTNTIQGMMVDTVTAVGKAGGFNV 72 Query: 63 TFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPY--YDNSALFVGQQGK-YT 119 F +LIPSL +++ + A M TP R++ V F+ P Y + G K Y Sbjct: 73 NVQQTVFSALIPSLTSSKIDIISAAMLKTPARQQVVDFSDPVYAYGEGLIVKGDDNKPYA 132 Query: 120 SVDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDGVFGDTAVVT 179 S+D+LKG+ VG Q GT + K YDS + DL GRI GD ++ Sbjct: 133 SLDELKGEVVGAQVGTVFLDMLNKKGIFKEVRSYDSVADMTRDLTLGRIKAGLGDQPIIA 192 Query: 180 EWLKDNP----KLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYET 235 ++ N KLAA V D + + VR+G+TE ++N A+ K+K DGT Sbjct: 193 YQIRQNAFPGVKLAASYKPVNVGD-----VCLVVRKGDTETLARINKAIAKIKADGTLAG 247 Query: 236 IYNKW 240 I KW Sbjct: 248 IIQKW 252 Lambda K H 0.316 0.133 0.380 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: 137 Number of extensions: 10 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: 243 Length of database: 254 Length adjustment: 24 Effective length of query: 219 Effective length of database: 230 Effective search space: 50370 Effective search space used: 50370 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 (21.6 bits) S2: 46 (22.3 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