Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 358 bits (919), Expect = e-103 Identities = 204/500 (40%), Positives = 304/500 (60%), Gaps = 12/500 (2%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L +SK FPGV+ALD VD + GE+ ALLGENGAGKSTLIK L+ + AD GT+ Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 69 EGQAISPKNTA-HAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRAT 127 GQ + P++ QQLGI T+YQE NL P +SVA+N+++GREP+R GL+ + A Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 L+ G L+ P+ +VA QQ+V I +A+ L+A+++I+DEPTA+L +EV+ L + Sbjct: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 + L+ R VS+I+V+H L +V + DR TV+R+G FV + ++ ++V++M+GR ++ Sbjct: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 Query: 248 THALQR---AGRTLLSDKPVA-AFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303 +R G +L + V A G + R GEIVGLAGL+G+GRT+ A Sbjct: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIIL-- 361 +IFG P +G L+ KP LRSP A GI PEDRK G S+R N+ L Sbjct: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362 Query: 362 --ALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLT 419 AL A W + + ++++ E + ++L I+ E I LSGGNQQKVLL R + Sbjct: 363 LKALSALGQW---VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419 Query: 420 RPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRK 479 P+ LI+DEPTRGID+GA AE+ +++ L G+A++VISSEL E++ +DR+++ R+ Sbjct: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479 Query: 480 QVAEIPLAELSVPAIMNAIA 499 VA++ + +M +A Sbjct: 480 IVADLDAQTATEEGLMAYMA 499 Lambda K H 0.321 0.138 0.391 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: 647 Number of extensions: 35 Number of successful extensions: 8 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: 500 Length of database: 515 Length adjustment: 34 Effective length of query: 466 Effective length of database: 481 Effective search space: 224146 Effective search space used: 224146 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 (21.8 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