Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 329 bits (844), Expect = 1e-94 Identities = 187/488 (38%), Positives = 287/488 (58%), Gaps = 8/488 (1%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 LEVV V K F GV AL V L + G + L+GENG GKSTL+KII+G PD G+L + Sbjct: 27 LEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 86 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 G P + L AL AGI ++Q+L+L+P+MS+AEN+ + E D + Sbjct: 87 GKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNG----LHMVDHGEMHR 142 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 AR LE + + + E Q + L +A RQ+V IA+A++ ++ +IMDEPT+++T+ EV Sbjct: 143 CTARLLERLRIKLDPEEQ---VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEV 199 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255 +L +++A+L++QG +++++HK++E +AI EV V RDG + + +M Sbjct: 200 AHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMM 259 Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315 GR LS D+VL VR + G F VSF LH GEILG+ GL+ SGR +A Sbjct: 260 VGRELSQLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAE 319 Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375 A+ GV P+ G++LLDGQ + + P A + EDR GLF + +N+ A++ Sbjct: 320 AIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 379 Query: 376 SSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 435 G I + +AL E K+L++ TP +++ + +LSGGNQQ+ L+ RWL +PR+ Sbjct: 380 PHYVGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 438 Query: 436 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAE 495 LIL PT G+DVG+K IYR++ L+ G+ +I+IS +LPE+L DR+++M +G + Sbjct: 439 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 498 Query: 496 YRADELSE 503 E ++ Sbjct: 499 LNRGEATQ 506 Score = 68.9 bits (167), Expect = 4e-16 Identities = 60/261 (22%), Positives = 116/261 (44%), Gaps = 19/261 (7%) Query: 1 MNQQEVSSAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKI 60 + +Q + LS L + G+ K GVS G+I + G G G++ + + Sbjct: 270 VREQPIGDLVLSVRDLSLDGIFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEA 320 Query: 61 ISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSL---LPNMSVAENVALTSEL 117 I G P G+++++G P A+ G + +D L P +SV EN+ E+ Sbjct: 321 IFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM----EM 376 Query: 118 ATHEGRLARTF-DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIAS 176 A + F ++ L A + + + S Q I+ L +Q +AR + + Sbjct: 377 AVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQC--IDTLSGGNQQKALLARWLMT 434 Query: 177 EAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQ 236 + +I+DEPT + + +++ L ++G+ V+ +S +L E + V+V+ +G Sbjct: 435 NPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGD 494 Query: 237 KMAQGPIAEFTKAQISELMTG 257 M E T+ ++ +L +G Sbjct: 495 LMGTLNRGEATQERVMQLASG 515 Lambda K H 0.319 0.135 0.376 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: 586 Number of extensions: 39 Number of successful extensions: 8 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: 515 Length of database: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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 (21.7 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