Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 360 bits (923), Expect = e-104 Identities = 207/492 (42%), Positives = 299/492 (60%), Gaps = 5/492 (1%) Query: 28 LEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 87 +E NV+K F V L V ++PG V L+GENGAGKSTLMKI+AG P GE+ + Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 88 GKPVTFDTPLAALQA-GIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 G A +A GI +IHQE NL ++IA+NI++G E G +D + M T Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGL-FLDDKAMREKTR 123 Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 + L ++ + LDP+ +V L +AE+Q+VEIA+A++ ++ +LIMDEPT+ +T E LF++ Sbjct: 124 EALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFAL 183 Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 +A LKA G IIYI+HK++EV DEV V RDG + + S+ + ++MVGREL+ Sbjct: 184 MAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRELA 243 Query: 267 QLFPVR--EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFG 324 LFP + G ++VR L + G +GV F++ GEILG AGL+G+GRT + E + G Sbjct: 244 DLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFEGLLG 303 Query: 325 ITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYA 384 + P G + + GQPV++ P A G L+EDRK GL + N+ + L YA Sbjct: 304 LRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALERYA 363 Query: 385 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDE 444 ++ A +A + ++ ++T SLE +LSGGNQQK LA+ L P +++LDE Sbjct: 364 -KPWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDE 422 Query: 445 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 504 PTRG+DVGAK EIY L+ LA +G+AVI+ISSEL E++G+ RV VM G L TL Sbjct: 423 PTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPH 482 Query: 505 ATQERVMQLASG 516 T+E ++ A+G Sbjct: 483 LTEEELIAHATG 494 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: 603 Number of extensions: 32 Number of successful extensions: 9 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: 496 Length adjustment: 34 Effective length of query: 487 Effective length of database: 462 Effective search space: 224994 Effective search space used: 224994 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