Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 275 bits (703), Expect = 3e-78 Identities = 164/472 (34%), Positives = 257/472 (54%), Gaps = 6/472 (1%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73 ++E + V+K F AL+DV +RV PG AL+G NGAGKSTL+ I+ G+ +PD GE+R Sbjct: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 Query: 74 SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG-GVIDWQAMRRDAR 132 G A + +A ++Q ++ +S+AEN++I R+ L G +ID + M R Sbjct: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192 LL+ +I++ + + G+LS+ RQ+VEIA+A+SY + +I+DEPT+ + E+ LF Sbjct: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGG 252 I++L+ +G ++I+H + EV+ I V V RD +I ++ + LI M G Sbjct: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 Query: 253 LAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAI 312 R D +++ L G ++GVSF + GE++G+ G SGRT+VAEAI Sbjct: 267 QLFP---VREKPIGDLLMSVRDLRLDGV-FKGVSFDLHAGEILGIAGLMGSGRTNVAEAI 322 Query: 313 AGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARV 372 G+ + G I +DG + D ++ G + +DR GL SV EN M + Sbjct: 323 FGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPH 382 Query: 373 LGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVL 432 G A + M L + E + LSGGNQQK ++AR L TNP +L+L Sbjct: 383 YAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILIL 442 Query: 433 IDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483 +PT G+DV +K + ++ + EG AV+++S EL + L DRV+VM G Sbjct: 443 DEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 494 Score = 58.2 bits (139), Expect = 7e-13 Identities = 58/242 (23%), Positives = 101/242 (41%), Gaps = 6/242 (2%) Query: 13 PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72 P+ + L + VS + GE + G G+G++ + + G+ D GE+ Sbjct: 275 PIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIC 334 Query: 73 FSGAAAPSIADRDAWRERVACVYQH---STIIRDLSVAENLFINRQP--LRGGVIDWQAM 127 G A + A + + S + LSV EN+ + P G I +A+ Sbjct: 335 LDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKAL 394 Query: 128 RRDARALLDHWKIDVREDARAGD-LSVEARQLVEIARALSYGARFIILDEPTAQLDGDEI 186 R + ++ + D LS +Q +AR L R +ILDEPT +D Sbjct: 395 RALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAK 454 Query: 187 KRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAM 246 ++R IS L EG+ + IS L EV + V V+ + + + S +E++++ Sbjct: 455 AEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLA 514 Query: 247 TG 248 +G Sbjct: 515 SG 516 Lambda K H 0.318 0.134 0.377 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: 529 Number of extensions: 23 Number of successful extensions: 6 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: 510 Length of database: 521 Length adjustment: 35 Effective length of query: 475 Effective length of database: 486 Effective search space: 230850 Effective search space used: 230850 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 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