Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate WP_025761778.1 X939_RS0102915 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >NCBI__GCF_000566685.1:WP_025761778.1 Length = 321 Score = 129 bits (323), Expect = 1e-34 Identities = 78/251 (31%), Positives = 140/251 (55%), Gaps = 16/251 (6%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 +QV + K YG + + +S A+ G L+G SGSGK+T L+ IN L +P G I +D Sbjct: 2 IQVNRVSKHYGSIKAVNRISFEAKLGSTTVLVGTSGSGKTTTLKTINRLIEPSEGQILID 61 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 G I +++ Q LR ++ V Q+ L+ H TV +N+ + P ++ SA Sbjct: 62 GKDISLQKP------------QLLRRQIGYVSQNNGLFPHYTVRQNVAIVP-SLIGWSAE 108 Query: 147 EAEKRARMYLDKVGLP-SRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDP 205 + +R+ L+++ +P ++ ++P LSGGQ QRVA+ARAL P ++L DEP ALDP Sbjct: 109 KTLQRSEEILEQLLIPMAQFGHKFPKELSGGQYQRVALARALVTRPPVLLMDEPFGALDP 168 Query: 206 ELVGEVLKVIQTL-AEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDAR-ILDQPN 263 ++ + +++L R++++VTH++ A ++ Q++ + +G+ + G A +L +P Sbjct: 169 VTRQQIRQELKSLPGHPERSIVLVTHDLAEAIELGDQIVVMDRGKCLQQGPASDLLFKPR 228 Query: 264 SERLQQFLSNR 274 ++ F + Sbjct: 229 DSFIKSFFDTQ 239 Lambda K H 0.319 0.133 0.372 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: 181 Number of extensions: 11 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: 276 Length of database: 321 Length adjustment: 26 Effective length of query: 250 Effective length of database: 295 Effective search space: 73750 Effective search space used: 73750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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