Align Inositol transport system ATP-binding protein (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 338 bits (867), Expect = 3e-97 Identities = 187/491 (38%), Positives = 297/491 (60%), Gaps = 5/491 (1%) Query: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 +L + I K + V L + L + G VLAL GENGAGKSTL KII G+ P G+++ Sbjct: 9 VLSVSGIGKTYAQPV-LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67 Query: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 +G+ + A++ GI M+ QELNL+P +S+AEN+++ N ++ +++ + Sbjct: 68 QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNG-GWISRKQLRKAAI 126 Query: 143 ELLARLRIN-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 +A++ ++ +DP+ VG L I +QMVEIA+ + D +LI+DEPT+ +T +EV LF Sbjct: 127 AAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186 Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 I L+++G I+YI+H++ E+ +A +AV RDG+ + ++ + NS+ L+++MVGREL Sbjct: 187 QITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGREL 246 Query: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321 + L IG LTV+ L+ +DVSF++ +GEI GI+GL+G+GRT + IFG Sbjct: 247 GEHIDLGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGA 306 Query: 322 TPSSSGQITLDGKA--VRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 + SG + L A V I P A+ G AL+TEDRK GL S+ N+ + +P Sbjct: 307 DAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVI 366 Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439 + G + AL + +R+++ S Q + LSGGNQQK ++ RWL +L+ D Sbjct: 367 SSGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLLFD 426 Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499 EPTRGIDVGAK +IY L+ L +G A++++SS+L E++ + DR+ V+ G L+ T +R Sbjct: 427 EPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERD 486 Query: 500 EATQEKVMQLA 510 TQ+ ++ A Sbjct: 487 SWTQDDLLAAA 497 Score = 89.7 bits (221), Expect = 2e-22 Identities = 61/226 (26%), Positives = 111/226 (49%), Gaps = 5/226 (2%) Query: 287 VFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIE 346 V + L GE+L + G G+G++ +++ I G+ ++GQ+ G+ R A E Sbjct: 23 VLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEE 82 Query: 347 KGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTP 406 G ++ ++ L P LSV EN+ + LP + G+I +K LR ++ + Sbjct: 83 LGIRMVMQELNL---LPTLSVAENLFLDNLP--SNGGWISRKQLRKAAIAAMAQVGLDAI 137 Query: 407 SLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMA 466 + + L G+QQ +AR L+ + +LILDEPT + ++ I L + G+A Sbjct: 138 DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVA 197 Query: 467 VIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 +I IS L E+ ++ R+ V+ +G L+ + E+++ L G Sbjct: 198 IIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVG 243 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: 580 Number of extensions: 31 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: 517 Length of database: 517 Length adjustment: 35 Effective length of query: 482 Effective length of database: 482 Effective search space: 232324 Effective search space used: 232324 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