Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 399 bits (1026), Expect = e-115 Identities = 217/496 (43%), Positives = 318/496 (64%), Gaps = 13/496 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 + + +GI K FPGV A+D+V F +Y E+ L+GENGAGKS+L+K+L GV DAGE Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +G V SP D GI+VI QE +L + +A+NIFL E RG+ + VD M Sbjct: 70 DGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREP-RGR---IPGSVDAARM 125 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + ++ +LD++G + S V L AQ+QMVEI KAL + RI+ +DEPT++L+ ETE Sbjct: 126 HAEARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETE 185 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 +LF +I LK+ G+S++++SHR+ EV + DRI ++RDG+++G G+ D ++ MV Sbjct: 186 KLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMV 245 Query: 254 GREVEF-FPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 GR+V+ + +PGE+AL+VRN+ + +++ +VR GE++G AGLVG+GR+E Sbjct: 246 GRKVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVAR 305 Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372 VFG + G+IY+ G+++ P+ A ++G LIPE RK +GL L TV+DN++L L Sbjct: 306 AVFGADPIRQGEIYIFGKRL-TGGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGL 364 Query: 373 KKI--SRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430 ++ +RW K E ++E + RL I TP Q+ + LSGGNQQK+V+ KWL A Sbjct: 365 RRAFPARW---YRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEA 421 Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490 + IFDEPTRGIDVGAKAEI +I L QG V++ISSELPEI+N+ DR VM G I Sbjct: 422 KLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIA 481 Query: 491 AVLDNREKRVTQEEIM 506 + + E +T+E I+ Sbjct: 482 GEVAHAE--MTEERIL 495 Score = 80.1 bits (196), Expect = 2e-19 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 28/246 (11%) Query: 25 PGVVAVD-----------NVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 PG VA+D +++ +V EIV L G G+G+S + + + G GEI + Sbjct: 261 PGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAVFGADPIRQGEIYI 320 Query: 74 NGERVEFHSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDE 130 G+R+ P A + G ++I + L TV +N+ LA G +R +R Sbjct: 321 FGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLLA-----GLRRAFPARW-- 372 Query: 131 NYMYTRSKELLDLIGAKF---SPDA--LVRNLTTAQRQMVEICKALVKEPRIIFMDEPTS 185 Y +++ L + A+ +PD L + L+ +Q + I K LV E ++ DEPT Sbjct: 373 -YRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIFDEPTR 431 Query: 186 SLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDV 245 + V +F +I+ L +G V+ +S L E++ + DR VMR G+ GE+ E Sbjct: 432 GIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHAEMTE 491 Query: 246 DTIIKM 251 + I+++ Sbjct: 492 ERILQL 497 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: 654 Number of extensions: 34 Number of successful extensions: 9 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: 502 Length adjustment: 35 Effective length of query: 485 Effective length of database: 467 Effective search space: 226495 Effective search space used: 226495 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 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