Align ABC transporter related (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 317 bits (812), Expect = 6e-91 Identities = 185/498 (37%), Positives = 282/498 (56%), Gaps = 9/498 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +LEL+ +S+ +PGV AL+ V +L GEVH L GENGAGKST++ ++ GA G+ F Sbjct: 23 LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 GEP N+ A+ GIS V+QE +LVP +TV +NLFLG E RLGL+ + ++ A A Sbjct: 83 RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRADA 142 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 +L + + + + A QQ++ IA+ VL+LDEPTASL +E LF ++ Sbjct: 143 ILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLI 202 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 Q+KA+GV +++ITH L ++ +I DRITVLR+G+++ P+ +L+ M GR E Sbjct: 203 EQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRVYDE 262 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDV-SVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 K R E LLS+E + + GS+ +L+V G+ VGLAGL+GSG+SEV Sbjct: 263 LF----PKVRFKPGRE--LLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVAR 316 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL--A 360 A FGL+ + G + L G+++ P + G P DR+ +G++ +REN+ L Sbjct: 317 ACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSL 376 Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420 A G L + + + ++L + P ++ +E SGGNQQKV+LA+ Sbjct: 377 TLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQ 436 Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVR 480 + DEPT G+D+G I + IR LC+ G +L+ SS+L E++ SN+ V Sbjct: 437 VFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQA 496 Query: 481 ELSGAELTSQHVMQAIAE 498 EL+G E+T + V+ E Sbjct: 497 ELAGDEITEEKVLSHFFE 514 Score = 54.3 bits (129), Expect = 1e-11 Identities = 59/251 (23%), Positives = 103/251 (41%), Gaps = 26/251 (10%) Query: 6 ELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLG 65 EL + + ++ + SL + AGE+ L G G+GKS + + G + G + G Sbjct: 274 ELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKG 333 Query: 66 E------PQH------FNTPMDAQKAGIST---VYQEVNLVPNLTVAQNLFLGYEPRRLG 110 E P+ F P D + G+ V + V+L P+LT+A P G Sbjct: 334 EEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSL-PSLTLA--------PFGNG 384 Query: 111 LIHFKKMYAD-ARAVLTQFKLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPT 168 + ++ D R + Q L + + +S QQ + +A+ +V DEPT Sbjct: 385 ALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPT 444 Query: 169 ASLDAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELP 228 +D ++ + L G I+ I+ L +V +S+R V G+ E E+ Sbjct: 445 VGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGDEIT 504 Query: 229 QPKLIEAMLGR 239 + K++ R Sbjct: 505 EEKVLSHFFER 515 Lambda K H 0.319 0.136 0.377 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: 582 Number of extensions: 30 Number of successful extensions: 7 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: 499 Length of database: 518 Length adjustment: 34 Effective length of query: 465 Effective length of database: 484 Effective search space: 225060 Effective search space used: 225060 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 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