Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 442 bits (1138), Expect = e-128 Identities = 237/493 (48%), Positives = 324/493 (65%), Gaps = 2/493 (0%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 +L++ VSK FPGVVAL + L +R G V A+ GENGAGKSTLMKII+G Y D G + Sbjct: 22 ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81 Query: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 GKPV F + A AGIA+IHQELNL+PH+S+AENI++ RE G +D+R ++ Sbjct: 82 EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRG-PFVDYRTLNANAQ 140 Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 + L+R+ +N+ P VG LSIA++QMVEIAKA+S D+ +LIMDEPTS++T+ E LF I Sbjct: 141 RCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 200 Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 I +L+A G I+YI+H+++E+ I D V V RDG +I S + +++ MVGR L Sbjct: 201 IRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRALD 260 Query: 267 QLFPVREK-PIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325 +P RE P +LM VRDL+ F +SFDL GEILG AGLMG+GRT VA AIFG Sbjct: 261 DAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFGA 320 Query: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAG 385 D G I L PV I P AI G A L+EDRK GL + V N+ ++ + + Sbjct: 321 ERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAISS 380 Query: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445 GF++ A+ E ++L ++TP+++Q LSGGNQQK ++++WL RIL DEP Sbjct: 381 RGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEP 440 Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505 TRGIDVGAK IY+L+ LA++G+ V++ISSELPE+LGM+DR+ V HEG + L+ + Sbjct: 441 TRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETRQT 500 Query: 506 TQERVMQLASGMS 518 +QE ++ ASG S Sbjct: 501 SQEEILHYASGRS 513 Score = 102 bits (253), Expect = 4e-26 Identities = 69/243 (28%), Positives = 123/243 (50%), Gaps = 15/243 (6%) Query: 286 LRLDGVFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLD 336 L+L GV K G+ DL +GE+ + G G+G++ + + I G +D G IC + Sbjct: 23 LQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICYE 82 Query: 337 GQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRA 396 G+PV+ + A G A++ ++ L P LSV EN+ +A P F+ + L A Sbjct: 83 GKPVQFASTSDAQAAGIAIIHQELNL---VPHLSVAENIYLAREPKRGP--FVDYRTLNA 137 Query: 397 LCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAE 456 + +++ + S + LS QQ +A+ L + R+LI+DEPT + + Sbjct: 138 NAQRCLQRIGLNV-SPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQ 196 Query: 457 IYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516 ++R+I L ++G+A++ IS L E+ + DRV V+ +G + T D + T ++ G Sbjct: 197 LFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVG 256 Query: 517 MSV 519 ++ Sbjct: 257 RAL 259 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: 656 Number of extensions: 19 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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