Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 419 bits (1078), Expect = e-121 Identities = 224/504 (44%), Positives = 332/504 (65%), Gaps = 12/504 (2%) Query: 10 DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69 D +L+ + K FPGVVA+ +V V +++L+GENGAGKSTL+KI+ G+ +PDAG Sbjct: 23 DEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 82 Query: 70 EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129 E+ + G+ V F +P+ A + GI++IHQELNL +M++AENI++ E + G +D Sbjct: 83 ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNG-----FHMID 137 Query: 130 ENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTV 189 M+ + +LL+ + P+ V NL+ A+RQMVEI KA+ + I+ MDEPTS++T Sbjct: 138 HREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITD 197 Query: 190 EETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249 +E LF II LK++G +++++H+++EV I+D + V RDG IG + D D++I Sbjct: 198 KEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLI 257 Query: 250 KMMVGREV-EFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGR 307 MMVGRE+ + FP + +P G++ + VR+L+ K VSF++ GE+LG AGL+G+GR Sbjct: 258 SMMVGRELSQLFP--VREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGR 315 Query: 308 TETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNI 367 T +FG+ + G+I ++G+ V I +P AI+ G L+ EDRKL GL ++V +N+ Sbjct: 316 TNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 375 Query: 368 VLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427 + L + G + ++ + ED K+L +KTPS+ Q + LSGGNQQK +LA+WL Sbjct: 376 EMAVLPHYAGNGFI-QQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 434 Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEG 487 TN ILI DEPTRGIDVGAKAEI+R+I LA++G AVIMISSELPE+L +SDR++VM EG Sbjct: 435 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 494 Query: 488 EITAVLDNREKRVTQEEIMYYASG 511 ++ LD E TQE +M ASG Sbjct: 495 DLMGTLDRSE--ATQERVMQLASG 516 Score = 96.7 bits (239), Expect = 2e-24 Identities = 61/233 (26%), Positives = 121/233 (51%), Gaps = 16/233 (6%) Query: 33 VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92 V F+++ EI+ + G G+G++ + + + G+ D GEI ++G+ V P A +KG + Sbjct: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354 Query: 93 VIHQELNLCDN---MTVAENIFLA---YEAVRG--QKRTLSSRVDENYMYTRSKELLDLI 144 ++ ++ L ++V EN+ +A + A G Q++ L + ++ R K Sbjct: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTP---- 410 Query: 145 GAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKS 204 S + + L+ +Q + + L+ PRI+ +DEPT + V ++ +I L S Sbjct: 411 ----SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLAS 466 Query: 205 RGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257 G++V+ +S L EV+ +SDR++VM +G +G L + E + ++++ G V Sbjct: 467 EGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519 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: 629 Number of extensions: 30 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: 521 Length adjustment: 35 Effective length of query: 485 Effective length of database: 486 Effective search space: 235710 Effective search space used: 235710 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