Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate 3608582 Dshi_1976 PfkB domain protein (RefSeq)
Query= reanno::Burk376:H281DRAFT_01116 (320 letters) >FitnessBrowser__Dino:3608582 Length = 305 Score = 349 bits (896), Expect = e-101 Identities = 181/301 (60%), Positives = 214/301 (71%) Query: 11 VVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGAEVVFCTRIGN 70 +VILGI+V D FRAAR P +GET+ G +FA+ PGGKGSNQA+AAA++G + F TR+G Sbjct: 5 IVILGIFVADCAFRAARPPRMGETVLGDSFALNPGGKGSNQAIAAAKSGGDARFLTRLGE 64 Query: 71 DAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGAAGTLSAADVD 130 DAF +A A WA G+ A A TGAA+I+VD TG NAIIVA GAA L AD+D Sbjct: 65 DAFADMAAAIWAEAGVRATAPRDPASYTGAAYIYVDPATGDNAIIVAPGAAALLGPADLD 124 Query: 131 AIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDDIFPLCDYITP 190 A I G+ VF+TQLEQP+ AARRGLE+AR GVTT+ NPAPA PLDD + LCD +TP Sbjct: 125 AQAEMIGGAGVFLTQLEQPMPAARRGLEIARAAGVTTILNPAPAAPLDDALLALCDIVTP 184 Query: 191 NETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQSIWLPAFRCG 250 NETEA ALTG P+ DDA RAAD LLA+G G VIVTLG G L ATQ+I PAF G Sbjct: 185 NETEAEALTGHPVTGPDDAVRAADALLARGPGAVIVTLGAQGVLYRSATQTIHQPAFTPG 244 Query: 251 AVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSMPTLAEVNRVL 310 VVET GAGD F G A ALA G+D SA+RFGCA A ISVTR G PSMP+ AE++ +L Sbjct: 245 PVVETTGAGDAFNGALATALAEGQDTASALRFGCATASISVTRPGAGPSMPSRAEIDALL 304 Query: 311 S 311 + Sbjct: 305 A 305 Lambda K H 0.318 0.132 0.377 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: 299 Number of extensions: 12 Number of successful extensions: 1 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: 320 Length of database: 305 Length adjustment: 27 Effective length of query: 293 Effective length of database: 278 Effective search space: 81454 Effective search space used: 81454 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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