Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 444 bits (1141), Expect = e-129 Identities = 235/493 (47%), Positives = 326/493 (66%), Gaps = 2/493 (0%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 +L++ VSK FPGVVAL + L + G V A+ GENGAGKSTLMKII+G Y+ D G +R Sbjct: 23 ILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRY 82 Query: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 RG PV F + A AGIA+IHQELNL+PH+S+AENI++ RE G +D+R ++ Sbjct: 83 RGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRG-PFVDYRTLNSNAQ 141 Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 + L+R+ +N+ P VG LS+A++QMVEIAKA+S D+ +LIMDEPTS++T+ E LF I Sbjct: 142 RCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 201 Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 I +L+A G I+YI+H+++E+ I D V V RDG +I S + +++ MVGR L Sbjct: 202 IRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRPLD 261 Query: 267 QLFPVREK-PIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325 +P R+ P +L+ VRDL+ GVF +SF+L GEILG AGLMG+GRT A AIFG Sbjct: 262 DAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFGA 321 Query: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAG 385 D G I L +PV I P AI G A L+EDRK GL + V N+ +A + + Sbjct: 322 ERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAISS 381 Query: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445 GF++ A+ E ++L ++TP+++Q LSGGNQQK ++++WL RIL DEP Sbjct: 382 RGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEP 441 Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505 TRGIDVGAK IY L+ LA++G+ V++ISSELPE+LGM+DR+ V HEG + L+ + Sbjct: 442 TRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETRQT 501 Query: 506 TQERVMQLASGMS 518 +QE ++ ASG S Sbjct: 502 SQEEILHHASGRS 514 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: 640 Number of extensions: 22 Number of successful extensions: 7 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: 516 Length adjustment: 35 Effective length of query: 486 Effective length of database: 481 Effective search space: 233766 Effective search space used: 233766 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