Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_068000557.1 PsAD2_RS00555 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IUD1 (522 letters) >NCBI__GCF_001623255.1:WP_068000557.1 Length = 522 Score = 384 bits (986), Expect = e-111 Identities = 207/495 (41%), Positives = 308/495 (62%), Gaps = 8/495 (1%) Query: 14 LTLSGIGKRYAA-PVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMMLD 72 L + G+ K + LDG+ L+ G+V AL GENGAGKSTL KI+ G+ +G + L+ Sbjct: 19 LDVQGVKKYFGGVKALDGVSFSLKQGEVHALVGENGAGKSTLIKILSGVYSFDSGNISLE 78 Query: 73 GQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPR-RFGWIDRKKLAEAARA 131 Y P S +A+ GI++V QE NL+ LSIAEN+ +E+LPR ++G +++ ++ AR Sbjct: 79 NTSYQPESPQEAKARGIQVVHQEFNLLEHLSIAENISIERLPRNKYGLLNKGEMNRRARE 138 Query: 132 QMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSR 191 ++ +GL ++D PVG LG+ H+Q++EIAR L + LILDEPTA LT RE + LF Sbjct: 139 ALDAIGLTDIDVRVPVGSLGIAHRQLIEIARALQSKSQILILDEPTATLTERETKRLFKI 198 Query: 192 IERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGELTK 251 I +++EGV ++++SH L+E+ I DR+ V R+GK V D I + E +VQ M G + Sbjct: 199 IAAIKSEGVTVVFVSHHLDEVFAICDRVTVFRNGKTVATDKISHMTPEGVVQRMVGRHLE 258 Query: 252 VDL--DAEHRRIGAPVLRIRGLGRAPVVHPA--SLALHAGEVLGIAGLIGSGRTELLRLI 307 + + G L+I + SL LH GE++GIAGL+GSGR+E+LR I Sbjct: 259 AGTRQHTDKQTFGPVALQIDAMRTMQNTGDTGISLNLHYGEIVGIAGLVGSGRSEILRGI 318 Query: 308 FGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANL 367 FG D G ++ E + P+DA+KAGI VTEDRK +GL+L I+ NTSL N+ Sbjct: 319 FGIDPIHSGTVY--RDGEEVNFKGPQDAIKAGIGFVTEDRKDEGLILDMPIAANTSLVNI 376 Query: 368 GSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIM 427 +S+ G++ E+ A++ +L+++ G A A LSGGNQQKVV+A+WL + ++ Sbjct: 377 HELSKTGLIQFTEENRQARESGSRLKLKYGKTADPASSLSGGNQQKVVLAKWLACNPKVL 436 Query: 428 LFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADTF 487 L DEPTRG+D+GAK++IY + +LA +G LLVVSS++ ELM + DRI V++ I Sbjct: 437 LLDEPTRGVDVGAKAEIYSILKDLAQEGVALLVVSSEMPELMTLADRIVVLAEHAIQGEL 496 Query: 488 SRDDWSQERILAAAF 502 ++S+E IL A+ Sbjct: 497 KPSEFSEENILKLAY 511 Score = 73.9 bits (180), Expect = 1e-17 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 5/224 (2%) Query: 30 GIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMMLDGQPYAPASRTQAEGLGI 89 GI L+L G+++ + G G+G+S + + I G+ +G + DG+ A GI Sbjct: 290 GISLNLHYGEIVGIAGLVGSGRSEILRGIFGIDPIHSGTVYRDGEEVNFKGPQDAIKAGI 349 Query: 90 RMVMQELN---LIPTLSIAENLFLEKLPR--RFGWIDRKKLAEAARAQMEVVGLGELDPW 144 V ++ LI + IA N L + + G I + AR + L Sbjct: 350 GFVTEDRKDEGLILDMPIAANTSLVNIHELSKTGLIQFTEENRQARESGSRLKLKYGKTA 409 Query: 145 TPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSRIERLRAEGVAIIY 204 P L G+QQ V +A+ L + + L+LDEPT + ++S ++ L EGVA++ Sbjct: 410 DPASSLSGGNQQKVVLAKWLACNPKVLLLDEPTRGVDVGAKAEIYSILKDLAQEGVALLV 469 Query: 205 ISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGE 248 +S + EL +ADRIVVL + + +S E +++L G+ Sbjct: 470 VSSEMPELMTLADRIVVLAEHAIQGELKPSEFSEENILKLAYGQ 513 Lambda K H 0.320 0.137 0.390 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: 632 Number of extensions: 32 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 522 Length of database: 522 Length adjustment: 35 Effective length of query: 487 Effective length of database: 487 Effective search space: 237169 Effective search space used: 237169 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: 52 (24.6 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