Align Inositol transport system ATP-binding protein (characterized)
to candidate H281DRAFT_01223 H281DRAFT_01223 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Burk376:H281DRAFT_01223 Length = 509 Score = 442 bits (1136), Expect = e-128 Identities = 237/506 (46%), Positives = 336/506 (66%), Gaps = 7/506 (1%) Query: 7 VSQPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLM 66 V QP S P+ LE+ + SK F V AL+D L + PG V AL+GENGAGKSTL+ Sbjct: 1 VQQPTSAVPR-------LELRHASKSFGRVRALSDGDLSLWPGEVHALLGENGAGKSTLV 53 Query: 67 KIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQL 126 KI+AG++QPD+GE+ + G F TP A+ AG+A+I+QE L +SIAENI++GR+ + Sbjct: 54 KILAGVHQPDSGELLVDGVARRFATPAQARDAGLAVIYQEPTLFFDLSIAENIFMGRQPV 113 Query: 127 NSLHMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDE 186 + + + M R LLA L ++L ++ V LSIA++Q++EIAKA+S ++++LIMDE Sbjct: 114 DRFGRIQYDAMRREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDE 173 Query: 187 PTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADS 246 PT+A++ EV LF+I+ L+ + I++ITH+++EVFA+ V + RDG + Sbjct: 174 PTAALSLTEVERLFAIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGMTAD 233 Query: 247 MNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGL 306 +N+D+++S MVGR+L +P E P G+ L+VR LT GVFKD+SFD+ AGEI+ +AGL Sbjct: 234 LNTDAIVSKMVGRDLETFYPKAERPPGEARLSVRGLTRVGVFKDISFDVRAGEIVALAGL 293 Query: 307 MGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLS 366 +G+GR+ VA IFGI P +GQI + GK + P A+ G AL+ EDR+ GL LS Sbjct: 294 VGAGRSEVARAIFGIDPLDAGQIQIGGKPLADGSPAAAVRAGLALVPEDRRQQGLALELS 353 Query: 367 VLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLA 426 + N M VL +G I ++ L +LR+K + LSGGNQQK +L Sbjct: 354 IARNASMTVLGRLVRHGLITTRSETQLANQWGTRLRLKAGDPNAPVGMLSGGNQQKVVLG 413 Query: 427 RWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMV 486 +WL TNP++LI+DEPTRGIDVGAKAE+Y +A L +GMAV+MISSELPEVLGM+DRV+V Sbjct: 414 KWLATNPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLV 473 Query: 487 MHEGELMGTLDRSEATQEKVMQLASG 512 MHEG + + R+EA +E++M A G Sbjct: 474 MHEGRISADIARAEADEERIMAAALG 499 Lambda K H 0.320 0.136 0.381 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: 638 Number of extensions: 24 Number of successful extensions: 5 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: 517 Length of database: 509 Length adjustment: 35 Effective length of query: 482 Effective length of database: 474 Effective search space: 228468 Effective search space used: 228468 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