Align ABC transporter related (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 363 bits (933), Expect = e-105 Identities = 194/492 (39%), Positives = 313/492 (63%), Gaps = 7/492 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +LE+ ISK +PGV AL DV LR+ G V AL+GENGAGKSTL+K++ G D G+I Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEP-RRLGLIHFKKMYADAR 122 G+P F TP+ AQKAGI+ ++QE+NL+P++++A+N+++G E L +++ ++M+ Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 +L + ++++D + + SIA +Q++ IA+ V+ + +L++DEPT+++ KEV LF I Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + LK++G IV+ITH +++V+ I+D + V R+G +IG + LI M+GR L Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 QL +E T +LL++ D+++ G + ++ + G+ +G+AGL+GSGR+ V Sbjct: 263 -QLFPLRE-----TPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAE 316 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362 +FG+ SG I L G+ + +S P AI G AL EDRK+ G+ LS+ EN+ +A+ Sbjct: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 376 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 ++ + + + KL++ TP ++ I+ LSGGNQQK +LARWL P LL Sbjct: 377 PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLL 436 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482 +LDEPTRGID+GA AEI +LI L EGM++++ SSEL E++ S++V+V+ + + L Sbjct: 437 ILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTL 496 Query: 483 SGAELTSQHVMQ 494 +E T + VMQ Sbjct: 497 DRSEATQEKVMQ 508 Score = 79.0 bits (193), Expect = 4e-19 Identities = 58/228 (25%), Positives = 109/228 (47%), Gaps = 14/228 (6%) Query: 21 EDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAG 80 +DVS L AGE+ + G G+G++ + + + G G I G+ + P A + G Sbjct: 289 KDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKG 348 Query: 81 ISTVYQE---VNLVPNLTVAQNLFLGYEPRRLG--LIHFKKMYADARAVLTQFKLDIDVS 135 + + ++ L P L+V +N+ + P G I K + RA+ + V Sbjct: 349 FALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKAL----RALCEDMCKKLRVK 404 Query: 136 APLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190 P + I QQ +AR + + ++L+LDEPT +D ++ ++ L ++G Sbjct: 405 TPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEG 464 Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238 +A++ I+ L +V +SDR+ V+ G+ +G +E Q K+++ G Sbjct: 465 MAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 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: 548 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: 517 Length adjustment: 34 Effective length of query: 465 Effective length of database: 483 Effective search space: 224595 Effective search space used: 224595 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