Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_061532804.1 CAter10_RS06720 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >NCBI__GCF_001584165.1:WP_061532804.1 Length = 515 Score = 414 bits (1063), Expect = e-120 Identities = 226/498 (45%), Positives = 328/498 (65%), Gaps = 9/498 (1%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG-ELR 85 +LE+ +SK F G+ L +V L V G V ALMGENGAGKSTLMK+++G +Q D G E+R Sbjct: 10 ILEMRGISKTFSGLRVLKEVDLTVYAGEVHALMGENGAGKSTLMKVLSGAHQADTGGEIR 69 Query: 86 LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCT 145 + G+ V P AA + G+A+I+QEL+L P++S+AENI++GRE G+ +D + M Sbjct: 70 IDGRRVVNYGPRAAKEHGVAVIYQELSLCPNLSVAENIYLGRELRQGWS-VDRKAMEAGC 128 Query: 146 AQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205 +L+RL + P +V +LSIAERQ+VEIA+A+ + IL+MDEPT+ ++ +E LF+ Sbjct: 129 VDVLKRLGADFTPHTKVSSLSIAERQLVEIARAIHAHARILVMDEPTTPLSSRETDRLFA 188 Query: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265 +I L+ +G I+YI+H+M E++ ++D V+V RDG ++G+ D + + L+ MMVGR+L Sbjct: 189 LIRQLREEGLAIVYISHRMAEIYELSDRVSVLRDGKHVGMLERDELSAEVLVKMMVGRDL 248 Query: 266 SQLFPVREKPI--GDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 323 S + P G+++M VRD+ +G SFDLHAGE+LGIAGL+G+GRT +A IF Sbjct: 249 SGFYKKEHAPYDPGNVVMRVRDMADGRRVRGCSFDLHAGEVLGIAGLVGAGRTELARLIF 308 Query: 324 GITPSDGGEICLDGQPV-RISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEM-AVLP 381 G P G + + GQ V + P AI G LTEDRK GLF +SV +N+ + A +P Sbjct: 309 GADPRIAGTLEVAGQAVSNLRGPADAIRAGVVYLTEDRKAQGLFLDMSVRDNINVCACVP 368 Query: 382 HYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILI 441 G + ++ + K L ++ S + LSGGNQQK LLAR L P +LI Sbjct: 369 DAGYGGVLDRRRGAQRAAEAIKSLSIRVASPGVNVGALSGGNQQKVLLARLLEIKPHVLI 428 Query: 442 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTL- 500 LDEPTRG+D+GAK+EIYR+I+ LA+ G+ V++ISSELPE++G SDRV+VM EG+L+ L Sbjct: 429 LDEPTRGVDIGAKSEIYRIINELANAGIGVVVISSELPEIVGTSDRVLVMREGELVAELG 488 Query: 501 --DRSEATQERVMQLASG 516 E TQE +++LA+G Sbjct: 489 GHSGREITQENIIELATG 506 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: 707 Number of extensions: 41 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: 515 Length adjustment: 35 Effective length of query: 486 Effective length of database: 480 Effective search space: 233280 Effective search space used: 233280 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