Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 5207771 Shew_0292 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__PV4:5207771 Length = 616 Score = 212 bits (539), Expect = 4e-59 Identities = 170/555 (30%), Positives = 261/555 (47%), Gaps = 71/555 (12%) Query: 44 GRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAAL-- 101 G+PI+ IA + + P + H ++ V I +AGGI EF + + + Sbjct: 33 GKPIVAIANSFTQFVPGHVHLKDMGSLVAGAIEEAGGIAKEFNTIAVDDGIAMGHGGMLY 92 Query: 102 ---DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGH 158 R L + +++ + D +V + CDK TP LMAA ++P + +SGGPM G Sbjct: 93 SLPSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGK 152 Query: 159 HK--GELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEA 216 K +LI V A A + E ++ +A P+ G C+ M TA SMN L EA Sbjct: 153 TKLSDKLIKLDLV--DAMVAAADDRVSDEDSEKIERSACPTCGSCSGMFTANSMNCLTEA 210 Query: 217 LGMSLPGCASIPAPYRERGQMAYATGKRICDLVRQDIR-------PSQIMTRQAFENAIA 269 LG+SLPG S+ A + +R ++ G+R+ L + R P I + +AFENA+A Sbjct: 211 LGLSLPGNGSLLATHSDRRELFLEAGRRVMALANRYYRDDDESALPRNIASFKAFENAMA 270 Query: 270 VASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPA-GKYLGEGFHRAG 328 + A+G SSN HL+A A+ V+ ++ D R+ VP L P+ KY E HRAG Sbjct: 271 LDIAMGGSSNTVLHLLAAAQEAKVDFTMADIDRLSRQVPHLCKVAPSTPKYHMEDVHRAG 330 Query: 329 GVPSVMHELQKAGRLHEDCATVSGKTI-GEIVSNSLTSNTD------------------- 368 GV ++ EL +AG LH D + V+G+ + +V L D Sbjct: 331 GVMGILGELDRAGLLHTDVSHVAGENLKAVLVQYDLVQTQDEAVQQFYAAGPAGIPTTKA 390 Query: 369 -----------------VIHPFDTPLKHRAGFIVLSGNF-FDSAIMKMSVVGEAFRKTYL 410 I + G VLSGN D I+K + V E Sbjct: 391 FSQSCRWPSLDVDRQEGCIRTREFAFSQEGGLAVLSGNIAADGCIVKTAGVDE------- 443 Query: 411 SEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAP 470 A ++F A V+E +D A I + + ++VIR G G PG E+ + P Sbjct: 444 ----ANHTFVGHARVYESQDDAVAGILGGEVVAGD--VVVIRYEGPKGGPGMQEM--LYP 495 Query: 471 PAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRT 529 + L +G+ S + DGR SG ++ SI ++SPEAA GG +AL++T DR+++D+ R+ Sbjct: 496 TSYLKSKGLGTSCALITDGRFSGGTSGLSIGHVSPEAAAGGTIALVETGDRIEIDIPARS 555 Query: 530 VNLLIDDAEMAQRRR 544 + L + D + RR+ Sbjct: 556 ITLAVSDEVLETRRQ 570 Lambda K H 0.319 0.135 0.407 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: 829 Number of extensions: 52 Number of successful extensions: 6 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: 594 Length of database: 616 Length adjustment: 37 Effective length of query: 557 Effective length of database: 579 Effective search space: 322503 Effective search space used: 322503 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: 53 (25.0 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