Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 315 bits (808), Expect = 2e-90 Identities = 176/501 (35%), Positives = 286/501 (57%), Gaps = 8/501 (1%) Query: 13 QPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQL 72 + L++ G+ K F GV AL G +L+ G++ L+GENG GKST++K+++G D G L Sbjct: 2 EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61 Query: 73 VIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRV 132 + G + AGI ++Q+L+L+P +++AEN+ L E G++ D + Sbjct: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKI----DWKT 117 Query: 133 LAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQ 192 + A A + L + L S+ L+ L + +Q+V IA+ ++ E+K +IMDEPT +LT Sbjct: 118 MYAEADKLLAKLNLRFKSD---KLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTD 174 Query: 193 KEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQIS 252 E ++L V+ L++QG ++++SH++ E + I +V V RDGQ +A+ +A T+ + Sbjct: 175 TETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLI 234 Query: 253 ELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNE 312 E+M GR L ++ DI L V G +DVSF L GEILGV+GL+ +GR E Sbjct: 235 EMMVGRKLEDQYPHLDKAPGDIRLKVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTE 293 Query: 313 LARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVIT 372 L + L G P SG V LDG ++ R+P D + I Y+ EDR +GL L +++N+ Sbjct: 294 LMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSL 353 Query: 373 AMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAID 432 + G + Q ++ + TP +++ + LSGGNQQ+V I R L Sbjct: 354 TALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTR 413 Query: 433 PRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHV 492 P+VLIL PT GVDVG+K IY+++ + G+ IIL+S ++PE+L DRI++M +GH+ Sbjct: 414 PKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHL 473 Query: 493 SAEYRADELSEADLYHALLSE 513 S E+ ++ ++ L A + + Sbjct: 474 SGEFTREQATQEVLMAAAVGK 494 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: 575 Number of extensions: 43 Number of successful extensions: 6 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: 515 Length of database: 501 Length adjustment: 34 Effective length of query: 481 Effective length of database: 467 Effective search space: 224627 Effective search space used: 224627 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