Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 582 bits (1501), Expect = e-171 Identities = 289/491 (58%), Positives = 378/491 (76%), Gaps = 2/491 (0%) Query: 26 YLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELR 85 + LE +SK FPGV AL +V LRVRPG+V ALMGENGAGKSTLMK + GIY+PD G +R Sbjct: 4 FALEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIR 63 Query: 86 LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCT 145 ++G+PV F + AL++GI+MIHQELNL+PHM++AENIW+GRE + + +DHR++ R T Sbjct: 64 VKGEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMK-YGFVDHRQLARQT 122 Query: 146 AQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205 LL++L I L + VG LSIA +QMVEIAKAVS+++DI+IMDEPTSA+T+ EVAHLF+ Sbjct: 123 QDLLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFT 182 Query: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265 II DL+ QGK IIYI+HKM+E+F+I DE++VFRDG ++G ++ SLI+ MVGREL Sbjct: 183 IIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGREL 242 Query: 266 SQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325 +QLFP IG+ +++VR+L G F ++F + GEILG+AGL+G+GR+ V E++FG+ Sbjct: 243 TQLFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGM 302 Query: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAG 385 +D GE+ +DG PV I P AIEKG ALLTEDRK SGLF LSVLENM + +P Y G Sbjct: 303 EKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIG 362 Query: 386 -NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDE 444 GF+Q + C + ++L +KTP+++Q I+ LSGGNQQK L+ARWL+ P+ILILDE Sbjct: 363 KTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDE 422 Query: 445 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 504 PTRGIDVGAKAEIY LIS LA+ G+AVIM+SSELPE+LGMSDRVMVMHEG + G LD+ + Sbjct: 423 PTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKED 482 Query: 505 ATQERVMQLAS 515 A QE ++ LAS Sbjct: 483 ADQETILSLAS 493 Lambda K H 0.321 0.137 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: 739 Number of extensions: 31 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: 1 Length of query: 521 Length of database: 494 Length adjustment: 34 Effective length of query: 487 Effective length of database: 460 Effective search space: 224020 Effective search space used: 224020 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