Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 317 bits (813), Expect = 5e-91 Identities = 180/503 (35%), Positives = 292/503 (58%), Gaps = 12/503 (2%) Query: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81 Y++E+ +I K FPG+VA +V L+V+ G + AL+GENGAGKSTLM ++ G+YQP+ GEI Sbjct: 3 YVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEIL 62 Query: 82 LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141 ++GKP+ P A + GI M+HQ L+ ++ ENI +G+E + +N ++ + Sbjct: 63 VKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEP-TAGGKINIKKAAKAV 121 Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 + + + +DP ++ ++S+ +Q VEI K + ++ILI DEPT+A+T +E+ L Sbjct: 122 ETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQ 181 Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 I+ L S+GK I+ ITHK+ E+ + D V R G IG DSL +MMVGRE+ Sbjct: 182 IMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241 Query: 262 SQLFPLRETPI--GDLLLTVRDLTLDG-----VFKDVSFDLHAGEILGIAGLMGSGRTNV 314 + F + + P D +L ++DL + D+ ++HAGEILG+AG+ G+G+T + Sbjct: 242 N--FSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTEL 299 Query: 315 AETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 374 E I G+ + G I L+G+ + P G + +DR GL +V EN+ + Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359 Query: 375 VL--PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTN 432 Y+ +G + + ++ + V+TPS LSGGNQQKA++AR + + Sbjct: 360 TYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRS 419 Query: 433 PRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGEL 492 P LLI +PTRG+DVGA I+ + +G AV++IS EL EVL +SDR+ V++EG++ Sbjct: 420 PDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKI 479 Query: 493 MGTLDRSEATQEKVMQLASGMTA 515 + +D + + ++ L +G +A Sbjct: 480 VAIVDADKTNENELGLLMAGGSA 502 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: 595 Number of extensions: 24 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: 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 Apr 09 2024. 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