Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 134 bits (338), Expect = 2e-36 Identities = 77/209 (36%), Positives = 127/209 (60%), Gaps = 9/209 (4%) Query: 36 DINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVDGIELTNDL--KKIDEVR 93 DI L + +GE I + GPSGSGK++ +R I+ L KG + V+G + + K + R Sbjct: 20 DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDASFGKNVSPGR 79 Query: 94 REVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFLERVKIPEQALKYPGQ 153 R++G +FQ ++LFP++T+ EN A + + + M LE + + P Sbjct: 80 RKLGYLFQDYSLFPNMTVKENIAFA------LKNAKDKAYLMELLESMGLLHLQDTLPKH 133 Query: 154 LSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVGLAEE-GMTMICVTHE 212 LSGGQQQRVA+AR+L ++P ILL DEP SALDP M +++ + ++ + + +T I V+H+ Sbjct: 134 LSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYALTTILVSHD 193 Query: 213 MGFARQVANRVIFMDQGQIVEQNSPAEFF 241 G ++++R+I +D G+++ Q +P EFF Sbjct: 194 AGEIIKLSDRIIELDHGKVLRQCTPKEFF 222 Lambda K H 0.322 0.136 0.397 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: 176 Number of extensions: 9 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: 258 Length of database: 290 Length adjustment: 25 Effective length of query: 233 Effective length of database: 265 Effective search space: 61745 Effective search space used: 61745 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 (21.9 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