Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 409 bits (1051), Expect = e-118 Identities = 223/490 (45%), Positives = 320/490 (65%), Gaps = 3/490 (0%) Query: 5 LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64 L+ GI K FPGVKAL G + +PG+V AL+GENGAGKST++K+L G YT +G L Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75 Query: 65 GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124 ++ F S +G+ +IHQEL+L+P++T+AEN+FLG FG I+ + +A Sbjct: 76 EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGH-LPASFGLINRGVLRQQALA 134 Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184 L L + VG LS+G +Q+VEIAK LS + VI DEPT +L+ E + L +I Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAERE-VASLTEDSLIEMMVGRKLE 243 L+ +G+ ++Y+SHRM+E+F IC+ VTVF+DG+F+ E +++LT D L+ MVGR ++ Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254 Query: 244 DQYPHLDKAPGDIRLKVDNLCGPGVND-VSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302 D Y + + G + LKVD L GPG+ + VSF KGEILG+ GL+GAGRTEL ++L G Sbjct: 255 DIYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLT 314 Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362 T+G + L G E+ SP+D +A GI+ EDRK++G++ SV EN++++A S Sbjct: 315 RNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTF 374 Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422 G L+ E+ I+ VKTP+ Q I LSGGNQQK + R L KVL+LDEP Sbjct: 375 GCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482 TRG+D+GAK EIYQ+I+ A G+++I+VSS++ EV+G+SDRI+V+ EG + GE TREQA Sbjct: 435 TRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQA 494 Query: 483 TQEVLMAAAV 492 + L+ A+ Sbjct: 495 NESNLLQLAL 504 Score = 79.0 bits (193), Expect = 4e-19 Identities = 57/234 (24%), Positives = 114/234 (48%), Gaps = 10/234 (4%) Query: 15 PGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPK 74 PG++ + + G ++ L G GAG++ + ++L+G+ AG L G+E P+ Sbjct: 277 PGLR--EPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPR 334 Query: 75 SSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKID---WKTMYAEADKLLA 127 + AGI + ++ ++P ++AENI + R + FG + W+ A+ Sbjct: 335 DAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKAL 394 Query: 128 KLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIREL 187 K+ + K++ LS G+QQ + + LS KV+++DEPT + ++++I L Sbjct: 395 KVKTPNAAQKIMY-LSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453 Query: 188 KSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241 + G ++ +S + E+ I D + V +G E E +L+++ + R+ Sbjct: 454 AASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 507 Lambda K H 0.318 0.137 0.380 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: 696 Number of extensions: 40 Number of successful extensions: 8 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: 501 Length of database: 514 Length adjustment: 34 Effective length of query: 467 Effective length of database: 480 Effective search space: 224160 Effective search space used: 224160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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