Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 347 bits (890), Expect = e-100 Identities = 194/485 (40%), Positives = 296/485 (61%), Gaps = 9/485 (1%) Query: 15 LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74 L+ GI K FPGV A+D + F + ++ +L+GENGAGKSTL+KIL G P +G++ + Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75 Query: 75 GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134 ++ F S D+ G++VIHQEL+L MTVAEN+FL G ++ + Sbjct: 76 EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFL------GHLPASFGLINRGVLR 129 Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194 ++ L + + P V L+ QRQ+VEI KAL + +I DEPTSSL+ E +R Sbjct: 130 QQALACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDR 189 Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKK-GEFDVDTIIKMMV 253 L II L+ G V++VSHR++EV RI + + V +DG+ + + D ++ MV Sbjct: 190 LMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMV 249 Query: 254 GREVEFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 GR+++ + +RP G +AL+V L + VSFE KGE+LG GLVGAGRTE Sbjct: 250 GRDIQDI-YDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFR 308 Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372 ++ G+ + +G + + GR++++ +P DAI GI L PEDRK +G++ +V +NI + + Sbjct: 309 MLSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISAR 368 Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432 S +G +L E++ ++ +K L +KTP+ Q LSGGNQQK +L +WL+ + Sbjct: 369 GAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKV 428 Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492 L+ DEPTRGID+GAKAEI+++I LAA G AVI++SS+L E++ +SDRI+V+ EG + Sbjct: 429 LLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGE 488 Query: 493 LDNRE 497 L + Sbjct: 489 LTREQ 493 Score = 96.3 bits (238), Expect = 2e-24 Identities = 64/229 (27%), Positives = 122/229 (53%), Gaps = 9/229 (3%) Query: 33 VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92 V FE ++ EI+ L G GAG++ L ++L+G+ + AG + + G ++ HSP DA GI Sbjct: 283 VSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGIL 342 Query: 93 VIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149 + ++ + +VAENI ++ RG T + + + + + + K + Sbjct: 343 LCPEDRKKEGILPLASVAENINIS---ARGAHSTFGCLLRGLWEKDNADKQIKALKVK-T 398 Query: 150 PDAL--VRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGI 207 P+A + L+ +Q + + L +++ +DEPT + + +++II L + GI Sbjct: 399 PNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGI 458 Query: 208 SVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGRE 256 +V+ VS L EVM ISDRI+V+ +G GEL + + + ++++ + R+ Sbjct: 459 AVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 507 Lambda K H 0.319 0.138 0.381 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: 661 Number of extensions: 36 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: 520 Length of database: 514 Length adjustment: 35 Effective length of query: 485 Effective length of database: 479 Effective search space: 232315 Effective search space used: 232315 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 (21.7 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