Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 419 bits (1078), Expect = e-121 Identities = 231/515 (44%), Positives = 333/515 (64%), Gaps = 16/515 (3%) Query: 3 PLLAFRGDRME----ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIK 58 P + FR D + +L+ + K FPGVVA+ +V V +++L+GENGAGKSTL+K Sbjct: 11 PAMTFRPDVIPDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMK 70 Query: 59 ILTGVLKPDAGEILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVR 118 I+ G+ +PDAGE+ + G+ V F +P+ A + GI++IHQELNL +M++AENI++ E + Sbjct: 71 IIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLN 130 Query: 119 GQKRTLSSRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRII 178 G VD M+ + LL+ + K P+ V NL+ A+RQMVEI KA+ + I+ Sbjct: 131 GLHM-----VDHGEMHRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDIL 185 Query: 179 FMDEPTSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGEL 238 MDEPTS++T E LF II LKS+G +++++H+++EV I+D + V RDG IG Sbjct: 186 IMDEPTSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQ 245 Query: 239 KKGEFDVDTIIKMMVGREV-EFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEV 296 + D D++I MMVGRE+ + FP + +P G++ L VR+L K VSF++ GE+ Sbjct: 246 RADSMDGDSLISMMVGRELSQLFP--VREQPIGDLVLSVRDLSLDGIFKGVSFDLHAGEI 303 Query: 297 LGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQG 356 LG AGL+G+GRT +FGV G+I ++G+ V I +P AI+ G L+ EDRKL G Sbjct: 304 LGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSG 363 Query: 357 LVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGN 416 L ++V +N+ + L G + ++ + ED K+L +KTPS+ Q + LSGGN Sbjct: 364 LFPCLSVLENMEMAVLPHYVGNGFI-QQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGN 422 Query: 417 QQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILN 476 QQK +LA+WL TN ILI DEPTRGIDVGAKAEI+R+I LA++G AVIMISSELPE+L Sbjct: 423 QQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLG 482 Query: 477 LSDRIVVMWEGEITAVLDNREKRVTQEEIMYYASG 511 +SDR++VM EG++ L+ E TQE +M ASG Sbjct: 483 MSDRVMVMHEGDLMGTLNRGE--ATQERVMQLASG 515 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: 632 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 520 Length of database: 517 Length adjustment: 35 Effective length of query: 485 Effective length of database: 482 Effective search space: 233770 Effective search space used: 233770 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