Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate WP_011373106.1 SUDEN_RS07715 autoinducer-2 kinase
Query= uniprot:Q97FW4 (500 letters) >NCBI__GCF_000012965.1:WP_011373106.1 Length = 520 Score = 228 bits (581), Expect = 4e-64 Identities = 157/505 (31%), Positives = 255/505 (50%), Gaps = 17/505 (3%) Query: 1 MRYLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQV---GWAEQNPENWWTACVKG 57 M+YL+ ID GT + +FD GN I + E+ + + + NW C + Sbjct: 1 MQYLMAIDAGTGSVRAVIFDMSGNQISVAQKEWTHLEEEGVPNSMSFDFKANWTLTC-QC 59 Query: 58 IREVIEKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIG 117 IR+ +E++ + DI + + G+VL DK+ + ++ D R +KE + + G Sbjct: 60 IRDSLERANLSGDDIAALSATSMREGIVLYDKDGDELW-AVANVDARADKEVRYLKENFG 118 Query: 118 --KEKLIRITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVS 175 +E+ +G G L +++W++NN PD Y+++ KV + D+I +L GV A + S Sbjct: 119 VIEEEFYAESGQTFALG-ALPRIMWLKNNRPDMYEKVAKVSMIGDWILARLCGVIATDPS 177 Query: 176 DASGTQMLDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVV 235 + T + + R+W+ ++ + + +I P V E + G V +KASKE+ L+VNT VV Sbjct: 178 NGGTTGIFSLKNRDWASDMSKKVGLKDDIFPKVLEVGTLMGSVTDKASKESGLSVNTKVV 237 Query: 236 GGAGDQAAGAIGNGIVREGLISTVIGT--SGVVFAATDT-PRFDSKGRVHTLCHAVPNKW 292 G GD G+ G G+V G + + G+ VV +T P D RV+ H V N+ Sbjct: 238 MGGGDVQLGSAGLGVVDVGQAAILGGSFWQQVVNIDKNTPPPLDMGIRVNP--HVVSNQS 295 Query: 293 HIMGVTQGAGLSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGI--IYLPY 350 G+T +GL + WF+ FC E LE+KE G+++Y LL EKAS+ GS GI I+ Sbjct: 296 QAEGITFFSGLVMRWFRDAFCDMEKLEAKEKGVDVYALLEEKASRVPVGSYGILPIFSDS 355 Query: 351 LMGERTPHIDPNVKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMK-VNIEEIR 409 + + H P+ + L N + F RS+ E LD I + V ++ I Sbjct: 356 MKYGKWYHAAPSFLNLNINPELCNRASMF-RSLQENAAIVSSINLDKIRDFTGVELDTIV 414 Query: 410 VSGGGAESSIWRQILSDIFNYELTTVKASEGPALGVAILAGVGAGIYNSVEEACDKIVKG 469 +GG ++ +W QILSD+ + + +E ALG A+ AGVG GIY + EA K+V Sbjct: 415 FAGGASKGLLWPQILSDVTGCRVKIPRVTEATALGGAMAAGVGIGIYKDITEAAKKLVVW 474 Query: 470 NEKVMPNANLIEVYSKVYEVYNSAY 494 + PN ++Y ++ + AY Sbjct: 475 DRVYEPNMENKKIYDEIKIKFEKAY 499 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: 673 Number of extensions: 36 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: 520 Length adjustment: 34 Effective length of query: 466 Effective length of database: 486 Effective search space: 226476 Effective search space used: 226476 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