Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 379 bits (972), Expect = e-109 Identities = 214/494 (43%), Positives = 299/494 (60%), Gaps = 3/494 (0%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 +L I VS+ F V L DV +RPG V AL+GENGAGKST MKI+AG P AGE+ L Sbjct: 5 VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64 Query: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 G+PV F + A AG+ MIHQE NL +++ ENI++GRE G +DHR M + Sbjct: 65 DGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRG-PFLDHRAMQAESR 123 Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 +LLERL +DP +V LS+ RQMVEIAKA+ + +LIMDEPT+ +T +E L Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183 Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 + L+A G I+Y +HK++EV IAD V V RDG + A + D + MVGRELS Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243 Query: 267 QLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 326 LFP + P + ++ V L + G + SF L GE+LG AGL+GSGRT + E I G+ Sbjct: 244 GLFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLR 303 Query: 327 PSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGN 386 P+ GE+ ++G P+ + A G LTEDRK GL + EN+ + L + G Sbjct: 304 PAT-GEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRF-GR 361 Query: 387 GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPT 446 I + A ++ +LSGGNQQK LLA+ ++ PR++I+DEPT Sbjct: 362 VLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPT 421 Query: 447 RGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEAT 506 RGIDVG K +IY I+ LA+EG +VI++SSELPEV+G+++RV+VM G + G ++ T Sbjct: 422 RGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAIT 481 Query: 507 QERVMQLASGMSVR 520 +E +++LA G++ R Sbjct: 482 EENIVRLAMGLNHR 495 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: 642 Number of extensions: 31 Number of successful extensions: 10 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: 521 Length of database: 499 Length adjustment: 34 Effective length of query: 487 Effective length of database: 465 Effective search space: 226455 Effective search space used: 226455 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 24 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