Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Length = 526 Score = 331 bits (848), Expect = 5e-95 Identities = 184/498 (36%), Positives = 293/498 (58%), Gaps = 9/498 (1%) Query: 7 SSAPLSQPFL-EVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65 ++ P+ +P+L E++ V K F GV AL V L + G + L+GENG GKSTL+KII+G Sbjct: 23 TATPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIY 82 Query: 66 PPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA 125 PD G+L + G P + L AL AGI ++Q+L+L+P+MS+AEN+ + E Sbjct: 83 QPDAGELRLRGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNG----L 138 Query: 126 RTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDE 185 D R + A+ LE + + + E L+ L +A RQ+V IA+A++ ++ +IMDE Sbjct: 139 HMIDHREMHRCTAKLLERLRINLDPE---ELVGNLSIAERQMVEIAKAVSYDSDILIMDE 195 Query: 186 PTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAE 245 PT+++T KEV +L +++A+L+ QG +++++HK++E ++I EV V RDG + Sbjct: 196 PTSAITDKEVAHLFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADS 255 Query: 246 FTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGL 305 + +M GR LS D++L VR G F DVSF LH GEILG+ GL Sbjct: 256 MDGDSLISMMVGRELSQLFPVREKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGL 315 Query: 306 LDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKP 365 + SGR +A A+ G+ P+ G++ LDG+ + + P A + EDR GLF Sbjct: 316 MGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLS 375 Query: 366 IRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLI 425 + +N+ A++ G I + +AL E K+L++ TP +++ + +LSGGNQQ+ L+ Sbjct: 376 VLENMEMAVLPHYVGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALL 434 Query: 426 GRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRIL 485 RWL +PR+LIL PT G+DVG+K IYR++ L+ G+ +I+IS +LPE+L DR++ Sbjct: 435 ARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVM 494 Query: 486 MMKKGHVSAEYRADELSE 503 +M +G + E ++ Sbjct: 495 VMHEGDLMGTLDRSEATQ 512 Score = 63.9 bits (154), Expect = 1e-14 Identities = 53/230 (23%), Positives = 105/230 (45%), Gaps = 10/230 (4%) Query: 32 RGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAG 91 + VS G+I + G G G++ + + I G P D G++ ++G A+ G Sbjct: 298 KDVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKG 357 Query: 92 IETVYQDLSL---LPNMSVAENVALTSELATHEGRLARTF-DRRVLAATAARALEAVGLP 147 + +D L P +SV EN+ E+A + F ++ L A + + + Sbjct: 358 FALLTEDRKLSGLFPCLSVLENM----EMAVLPHYVGNGFIQQKALRALCEDMCKKLRVK 413 Query: 148 GNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRA 207 S Q I+ L +Q +AR + + + +I+DEPT + + +++ L + Sbjct: 414 TPSLEQC--IDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLAS 471 Query: 208 QGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257 +G+ V+ +S +L E + V+V+ +G M +E T+ ++ +L +G Sbjct: 472 EGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 521 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: 37 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: 526 Length adjustment: 35 Effective length of query: 480 Effective length of database: 491 Effective search space: 235680 Effective search space used: 235680 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