Align ABC transporter related (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 360 bits (925), Expect = e-104 Identities = 191/492 (38%), Positives = 311/492 (63%), Gaps = 7/492 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +LE+ +SK +PGV AL DV LR+ G V AL+GENGAGKSTL+K++ G D G++ Sbjct: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRR-LGLIHFKKMYADAR 122 G+P F+TP+ A +AGI+ ++QE+NL+P++++A+N+++G E +I ++M+ Sbjct: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 +L + ++++D + + SIA +Q++ IA+ V+ + +L++DEPT+++ KEV LF I Sbjct: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + LKA+G I++ITH +++V+ I+D + V R+G +IG + LI M+GR L Sbjct: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 QL +EK +L+S+ D+ + G + ++ + G+ +G+AGL+GSGR+ V Sbjct: 267 -QLFPVREKP-----IGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAE 320 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362 A+FG+ D G I L GQ + +S P AI G AL EDRK+ G+ LS+ EN+ +A+ Sbjct: 321 AIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 380 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 ++ + + + KL++ TP ++ I+ LSGGNQQK +LARWL P +L Sbjct: 381 PHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRIL 440 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482 +LDEPTRGID+GA AEI +LI L EGM++++ SSEL E++ S++V+V+ + + L Sbjct: 441 ILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTL 500 Query: 483 SGAELTSQHVMQ 494 +E T + VMQ Sbjct: 501 DRSEATQERVMQ 512 Score = 84.7 bits (208), Expect = 7e-21 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 14/230 (6%) Query: 23 VSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAGIS 82 VS L AGE+ + G G+G++ + + + G D G+I G+P + P A + G + Sbjct: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354 Query: 83 TVYQE---VNLVPNLTVAQNLFLGYEPRRLG--LIHFKKMYADARAVLTQFKLDIDVSAP 137 + ++ L P L+V +N+ + P G I K + RA+ + V P Sbjct: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKAL----RALCEDMCKKLRVKTP 410 Query: 138 LSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKGVA 192 + I QQ +AR + + ++L+LDEPT +D ++ +++ L ++G+A Sbjct: 411 SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMA 470 Query: 193 IVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 ++ I+ L +V +SDR+ V+ G +G +E Q ++++ G S++ Sbjct: 471 VIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSVR 520 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: 571 Number of extensions: 25 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: 521 Length adjustment: 34 Effective length of query: 465 Effective length of database: 487 Effective search space: 226455 Effective search space used: 226455 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 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