Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 269 bits (687), Expect = 2e-76 Identities = 171/493 (34%), Positives = 263/493 (53%), Gaps = 24/493 (4%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73 +++ +V+K F AL+ V + V GE HAL+G NGAGKSTL+ IL+ D G V F Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 74 SGAAAPSIADRDAWRER----VACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRR 129 +G + RDA R +A +YQ + +LSVAEN+++ R+P R G++DW +R Sbjct: 63 AGQV---LDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 Query: 130 DARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189 DA+ALL+ + + DA L+V +Q+VEIA+A++ AR II+DEPTA L G E+ RL Sbjct: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 Query: 190 FRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGE 249 I+ L+ V+ +++SH L EV +C TV+RD R + S V+ + ++ M G Sbjct: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239 Query: 250 RGGLAVADAAARGALPADTAVALELKELTGAD--------YEGVSFTVKRGEVVGLTGAT 301 + R AV L+++ +T A VSF + GE+VGL G Sbjct: 240 H-----VEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLV 294 Query: 302 SSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSV 361 +GRT +A I G G + VD L ++ GI VP+DR +G L S+ Sbjct: 295 GAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSI 354 Query: 362 AENASMTIARVLGKFG--IAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVM 419 N S+ + L G + A+++ + L I E + LSGGNQQKV++ Sbjct: 355 RRNLSLPSLKALSALGQWVDERAERDLV-ETYRQKLRIKMADAETAIGKLSGGNQQKVLL 413 Query: 420 ARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVL 478 RA+A P VL++ +PT G+D+ +K + V+ + + G AV+V+S EL + + DR++ Sbjct: 414 GRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIV 473 Query: 479 VMFRGRVAAEFPA 491 V G + A+ A Sbjct: 474 VFREGVIVADLDA 486 Score = 55.8 bits (133), Expect = 4e-12 Identities = 57/243 (23%), Positives = 95/243 (39%), Gaps = 9/243 (3%) Query: 23 RFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIA 82 R + L VS GE L G GAG++ L ++ G G V + Sbjct: 268 RLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRS 327 Query: 83 DRDAWRERVACVYQ---HSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK 139 RDA + + V + D S+ NL + + W R + R L++ ++ Sbjct: 328 PRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAE-RDLVETYR 386 Query: 140 IDVR-----EDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRIS 194 +R + G LS +Q V + RA++ + +I+DEPT +D + + +S Sbjct: 387 QKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLS 446 Query: 195 ELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLA 254 +L GV + IS L EV + + V R+ + E L+ M +A Sbjct: 447 DLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATGTDRVA 506 Query: 255 VAD 257 D Sbjct: 507 APD 509 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: 609 Number of extensions: 26 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: 510 Length of database: 515 Length adjustment: 35 Effective length of query: 475 Effective length of database: 480 Effective search space: 228000 Effective search space used: 228000 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