Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate HSERO_RS04850 HSERO_RS04850 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS04850 Length = 362 Score = 429 bits (1104), Expect = e-125 Identities = 218/360 (60%), Positives = 274/360 (76%), Gaps = 7/360 (1%) Query: 1 MARISL-DLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLV 59 MARI +L H+Y NP DYAL P+ M +EDGGAYALLGPSGCGK+T+LNI+SGLL Sbjct: 1 MARIEFKNLGHAYSGNPASLKDYALQPMNMVWEDGGAYALLGPSGCGKSTLLNIISGLLQ 60 Query: 60 PSHGKVLFDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRV 119 PS G+VLFDGRD+TR + ++RNIAQVFQFPV+YDTM+V +NLAFPLRNRK+ E +++ RV Sbjct: 61 PSEGQVLFDGRDMTRMATRDRNIAQVFQFPVLYDTMSVFDNLAFPLRNRKIAEREVQARV 120 Query: 120 GVIAEMLEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLR 179 IAEML+++ L QRAAGL+ADAKQKISLGRGLVR DVAA+LFDEPLTVIDPH+KW+LR Sbjct: 121 REIAEMLDLTRDLKQRAAGLSADAKQKISLGRGLVRKDVAAILFDEPLTVIDPHMKWELR 180 Query: 180 RKLKQIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHF 239 +KLK+IHH+LKLTLIYVTHDQVEALTFAD+VVVMT GK VQ G +ALF RP HTFVG+F Sbjct: 181 QKLKEIHHQLKLTLIYVTHDQVEALTFADEVVVMTEGKVVQQGKPEALFLRPDHTFVGYF 240 Query: 240 IGSPGMNFLPAHRDGENLSVAGHRLASPVGRALPA----GALQVGIRPEYLALAQPQQAG 295 IGSPGMNF P +G+ + + RL + G L++GIRPE++ LA P G Sbjct: 241 IGSPGMNFCPVRLEGDAVLLGQQRLQIEAAQLQALKNSNGELKLGIRPEFVELAAPGATG 300 Query: 296 ALPGTVVQVQDIGTYQMLTAKVGEHTVKARFTPETRLPSSGDTAWLQVLGEHTCYYKNEE 355 A+ + QVQ +GT Q++TA+ +VKAR +PE ++ + WL++ T Y+ N+E Sbjct: 301 AVSAEITQVQHLGTSQLVTAQFEGMSVKARLSPEMKIATGNQ--WLRLAKPETIYFSNDE 358 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: 403 Number of extensions: 13 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: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 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 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