Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 429 bits (1102), Expect = e-124 Identities = 239/498 (47%), Positives = 323/498 (64%), Gaps = 10/498 (2%) Query: 33 VSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVT 92 +SK F GV AL DV+ +R G + ALMGENGAGKSTLMK+++G+Y G +R+ G+ V Sbjct: 24 ISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAVRVDGETVR 83 Query: 93 FDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLERL 152 F A AGIA+IHQELNL+P + +A+NI++GRE++ +D + LL RL Sbjct: 84 FSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKASLEAARGLLNRL 143 Query: 153 RINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKA 212 I LDPE +VG L + E+Q+VEIAKA+S ++ ILIMDEPTSA++ E LF I+ L A Sbjct: 144 GIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRLFKIMRQLAA 203 Query: 213 QGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELSQLF-PV 271 G GIIYI+H+++EV ++D V VFRDG ++ + +D +++I+ MVGR L Sbjct: 204 DGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTIIAAMVGRNLLDAHRRD 263 Query: 272 REKPIGDLLMSVRDLRL--------DGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 323 R K G+ ++SVRDL L V KGVSFD+ AGEILGI GL+G+GRT + E IF Sbjct: 264 RGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTEILETIF 323 Query: 324 GITPS-DGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPH 382 GGEI LDG V I P A GFAL+TEDRK GL S+ +N+ + ++ Sbjct: 324 ASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVALPLVGR 383 Query: 383 YAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILIL 442 A G + RAL + L V+ Q TLSGGNQQK ++ +WL T PR+L+L Sbjct: 384 LARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWLATGPRVLLL 443 Query: 443 DEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDR 502 DEPTRGIDVGAK EIY LI LA +G+A++++SSELPE+L ++DR++VM EG G + R Sbjct: 444 DEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEGRQTGLISR 503 Query: 503 SEATQERVMQLASGMSVR 520 EA++ER+MQLA+ S R Sbjct: 504 EEASEERIMQLAAPRSAR 521 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: 704 Number of extensions: 39 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: 521 Length of database: 526 Length adjustment: 35 Effective length of query: 486 Effective length of database: 491 Effective search space: 238626 Effective search space used: 238626 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