Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS07685 (263 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 157 bits (396), Expect = 4e-43 Identities = 96/247 (38%), Positives = 149/247 (60%), Gaps = 18/247 (7%) Query: 16 DIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQIVVDGEMV 75 +I K G +K +L+ N+G++ I+G SGSGKST LRCIN L RP +G+++++G Sbjct: 32 EILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIING--- 88 Query: 76 KTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVLGLKRKEAE 135 TD A +V+D + LQ R +LAMVFQ+F L H +VL NI + + G+K+ E E Sbjct: 89 ---TDIA---KVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFG-LELQGVKKGERE 141 Query: 136 DRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALDP---- 191 +A E ++ VGL E Q S LSGG QQRV +ARALA NP+V+L DE SALDP Sbjct: 142 QKAMESMQLVGL-KGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRV 200 Query: 192 ELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEVLSAPRS 251 ++ E+L + K+ +T++ +TH++ A + + + + G + G E+L+ P + Sbjct: 201 QMQDELLTLQSKMK---KTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPAN 257 Query: 252 ERLKQFL 258 +++F+ Sbjct: 258 AYVERFV 264 Lambda K H 0.318 0.133 0.374 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: 217 Number of extensions: 11 Number of successful extensions: 5 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: 263 Length of database: 408 Length adjustment: 28 Effective length of query: 235 Effective length of database: 380 Effective search space: 89300 Effective search space used: 89300 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: 48 (23.1 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