Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 319 bits (817), Expect = 2e-91 Identities = 193/474 (40%), Positives = 284/474 (59%), Gaps = 18/474 (3%) Query: 37 LCGGNGAGKSTFLSILMGITQRDAG--SILLNGAPV-QFNRPSEALAAGIAMITQELEPI 93 L G NGAGKST L IL G DAG S+ NG + + + P GI I QE I Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 94 PYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDVDATSPMHRLSVAQIQLVE 153 M+VAEN++LGREP R G VD K + + +LD L + + + +LSVA+ Q+VE Sbjct: 61 ADMSVAENMYLGREPLRHG-FVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVE 119 Query: 154 IAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDY 213 IAKA + + +++IMDEPT+A+ E L + I L A+G I+YVSH+L+E+ D Y Sbjct: 120 IAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRY 179 Query: 214 SIFRDGAFVESGRMADIDRDHLVRGIVGQELTRIDHKVGRECAANTCLQVDNLSR----- 268 +IFRDGA++ SG + D+ D +VR +VG+++ + K L+V ++SR Sbjct: 180 TIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFV-RKPLTGAPGEVMLKVQSVSRTAAGG 238 Query: 269 -----AGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPM-PI 322 A D+S+ +R GEI+G GL+G+GR+E I+G D G + + G+ + P Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPF 298 Query: 323 GLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSL-INARKETQLAEDM 381 P+ I AG++LV EDRK L+ SI N++L + L W + I+ R ETQL +D Sbjct: 299 KSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDY 358 Query: 382 VKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLL 441 KRL+IK ++ + + ++SGGNQQKV+LA+C++ +P L+ DEPTRGID GAK E++ LL Sbjct: 359 QKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLL 418 Query: 442 DQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV-TISTDTALSQEALLRLA 494 R G A IV+SSE PE++ +SDRI F+ G++ +S D A + + R+A Sbjct: 419 FDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMA 472 Score = 69.7 bits (169), Expect = 2e-16 Identities = 55/228 (24%), Positives = 102/228 (44%), Gaps = 13/228 (5%) Query: 5 LLLQAEHVAKAYAG------VPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQR 58 ++L+ + V++ AG L D + +RAG + G GAG++ ++ G Sbjct: 224 VMLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGC 283 Query: 59 DAGSILLNGAPVQ-FNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREP-----RRAG 112 D G I +NG V F P E +AAG+A++ ++ + W P +R G Sbjct: 284 DEGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWG 343 Query: 113 CIVDNKALNRRTRELLDSLEFDVDATS-PMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPT 171 +D++A + ++ L + S + LS Q V +A+ + +V+I+DEPT Sbjct: 344 MFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPT 403 Query: 172 SAIGEHEAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDG 219 I + + + + G ++ +S L E+ ++D FR+G Sbjct: 404 RGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREG 451 Lambda K H 0.319 0.135 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: 599 Number of extensions: 33 Number of successful extensions: 11 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: 495 Length of database: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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