Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 145 bits (367), Expect = 9e-40 Identities = 80/211 (37%), Positives = 122/211 (57%), Gaps = 8/211 (3%) Query: 1 MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60 M+ + + V++ F+ + ++ V D +FV ++GPSGCGKST LR++AGL+ Sbjct: 1 MAEIKLDQVNKRFK-----KNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEV 55 Query: 61 TSGRVLLDGAPVEG-PGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAA 117 TSG + + G V P +R MVFQSY L+P + + +N+ FGL RG+P + R Sbjct: 56 TSGEISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVK 115 Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177 +G+ Q P QLSGG +QR A+ RA+ DP+ L DEP LD + RV M+ Sbjct: 116 QAAEILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAE 175 Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAV 208 L + E + T+++VTHD EA+ +A+R+ V Sbjct: 176 LAKLHERLQSTIVYVTHDQIEAMTLADRIVV 206 Lambda K H 0.322 0.136 0.394 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: 214 Number of extensions: 8 Number of successful extensions: 2 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: 259 Length of database: 368 Length adjustment: 27 Effective length of query: 232 Effective length of database: 341 Effective search space: 79112 Effective search space used: 79112 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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