Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_007695653.1 C447_RS15655 ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000336675.1:WP_007695653.1 Length = 332 Score = 125 bits (315), Expect = 9e-34 Identities = 77/253 (30%), Positives = 134/253 (52%), Gaps = 24/253 (9%) Query: 4 LEVQDLHKRY-GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 + ++HK+Y + G + G ++G SG GK+T +R +N LE+P G I Sbjct: 2 IRFDNVHKQYPDGTRAVDGHDFEVEEGTTTVLVGPSGCGKTTTMRLVNRLEEPTEGTIYY 61 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + +++ L+A D +R + V Q L+ HMT EN+ P + G Sbjct: 62 DGTDIE-------ELEATD------LRREIGYVIQDIGLFDHMTVGENVATVP-ELKGWE 107 Query: 123 KTEAREKAEHYLNKVGVAHR--KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180 ++ + L +G+ +D+YPG +SGG+QQRV +ARALA P+VML DEP AL Sbjct: 108 AERTADRVDELLELMGLPPEEFRDSYPGELSGGQQQRVGVARALAAGPDVMLMDEPFGAL 167 Query: 181 DP----ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREV 236 DP EL + L + + + T+V VTH++ A ++ +++ +++G V + P + Sbjct: 168 DPITREELQDEFLDIQKEI---DTTIVFVTHDINEALKMGDKIAVMNEGKVVQYDTPTAL 224 Query: 237 LVNPQSERLQQFL 249 L NP+++ +++F+ Sbjct: 225 LDNPKTKFVEEFI 237 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: 194 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: 254 Length of database: 332 Length adjustment: 26 Effective length of query: 228 Effective length of database: 306 Effective search space: 69768 Effective search space used: 69768 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 24 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