Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 120 bits (300), Expect = 7e-32 Identities = 87/291 (29%), Positives = 142/291 (48%), Gaps = 14/291 (4%) Query: 27 LKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGK------VLFDGRDVTRASPQER 80 L +E +G LLGPSGCGKTT L +++G P+ GK V++D R P++R Sbjct: 24 LNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIRIGDEVVYDDRRAL--PPEKR 81 Query: 81 NIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLA 140 I VFQ ++ +T+ +N+ F L K + K+R + E++ + ++ + L+ Sbjct: 82 GIGMVFQDYALFPHLTIEKNVTFGLNRWKNRDK--KKRAQEVLELVGLGEFGHRLPSELS 139 Query: 141 ADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQ 200 +Q+++L R L +L DEP + +D L+ ++R + I + T I VTHDQ Sbjct: 140 GGQQQRVALARALAPRP-KVILMDEPFSNLDAGLREKMRYDVTNILRKANATAIIVTHDQ 198 Query: 201 VEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVA 260 +A +D+VVVM G Q+ + ++ PA+ FV F+G + D +++ Sbjct: 199 KDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFVGKTNLISGTLCPDLKHVETH 258 Query: 261 GHRLASPVGRALPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQ 311 R+ P + V IRPE LA + G G V +V G YQ Sbjct: 259 IGRVCLPQETDKVIENVMVSIRPEGCRLA---EKGRYAGLVERVTYSGEYQ 306 Lambda K H 0.320 0.136 0.395 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: 266 Number of extensions: 7 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: 358 Length of database: 351 Length adjustment: 29 Effective length of query: 329 Effective length of database: 322 Effective search space: 105938 Effective search space used: 105938 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: 49 (23.5 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