Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate WP_010531875.1 ON01_RS14910 xylulose kinase
Query= uniprot:Q97FW4 (500 letters) >NCBI__GCF_000224785.1:WP_010531875.1 Length = 496 Score = 211 bits (538), Expect = 4e-59 Identities = 154/504 (30%), Positives = 238/504 (47%), Gaps = 19/504 (3%) Query: 3 YLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIREVI 62 Y D+GT+ K AL + T E E G EQNP +WW + Sbjct: 4 YAAVFDIGTTAVKGALVRNDASFYSERTVELETHYAPDGIVEQNPNDWWDGVKFIAHQWW 63 Query: 63 EKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEKLI 122 +++ +DP + I +GQM ++ I +++ + +I++ D R E + +++ Sbjct: 64 KEAGVDPGQVAIISFTGQMEDVIPIT-QHQTVNRAILYSDTRAVSEAEWLHQQF--PEMV 120 Query: 123 RITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLL-PKDYIRFKLTGVFAAEVSDASGTQ 181 ++TGNP L+KLL ++N Y L KD++ ++LTG A + + A+ T Sbjct: 121 QMTGNPISATTPLAKLLQMKNRNQKIYDDTRCFLFGSKDFMIYRLTGAIATDPTTAATTG 180 Query: 182 MLDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGDQ 241 M+D+ TR W ++ ID LP + ++ G V ++A+ ET TPV+ G GD Sbjct: 181 MMDVRTRRWETDIFSLTGIDTEKLPRILDAADPVGYVHKEAALETGFRPETPVLCGCGDA 240 Query: 242 AAGAIGNGIVREGLISTVIGTSGVVFAATD--TPRFDSKGRVHTLCHAVPNKWHIMGVTQ 299 AA AIG G V+ G IGT+G + + P S G H L H + Sbjct: 241 AASAIGAGAVKSGDSYCYIGTTGWIAGIQEDVNPEAASHGLFH-LAHLPEKSIISVAPLL 299 Query: 300 GAGLSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHI 359 AG W TF ++ + A ++ L QS PGSNG+++LPYL GER P Sbjct: 300 NAGNVYQWGADTFAEGQVNDRFHA----FEALIR---QSAPGSNGVLFLPYLQGERNPVN 352 Query: 360 DPNVKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSI 419 D KGAF GI D R+I+EG+ FSLK ++++ N++ N + + GGG +SS Sbjct: 353 DQQAKGAFWGIGPQTKKCDLARAIIEGICFSLKQVMEVL-NLESN-DVLTTVGGGTKSST 410 Query: 420 WRQILSDIFNYELTTV-KASEGPALGVAILAGVGAGIYNSVEEACDKIVK--GNEKVMPN 476 W Q L+DI + + S ALG A + G N E+ D+ + +E P+ Sbjct: 411 WCQTLADILERPVRIAPENSYMSALGAVSPAFLQLGWTNDYEDFTDRFINMPVSEIFEPS 470 Query: 477 ANLIEVYSKVYEVYNSAYPKIKDI 500 N VY Y+ + YP +K I Sbjct: 471 QNTFAVYRDQYKQFLKMYPGLKGI 494 Lambda K H 0.317 0.136 0.404 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: 544 Number of extensions: 21 Number of successful extensions: 5 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: 500 Length of database: 496 Length adjustment: 34 Effective length of query: 466 Effective length of database: 462 Effective search space: 215292 Effective search space used: 215292 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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