Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__SB2B:6939185 Length = 618 Score = 206 bits (523), Expect = 3e-57 Identities = 174/570 (30%), Positives = 267/570 (46%), Gaps = 83/570 (14%) Query: 44 GRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAAL-- 101 G+PII IA + + P + H ++ V + I +AGGI EF + + + Sbjct: 33 GKPIIAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLY 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 I ++ +A P+ G C+ M TA SMN L EA Sbjct: 153 TKLSDKLIKLDLV--DAMVAAADDRISDADSEKIERSACPTCGSCSGMFTANSMNCLTEA 210 Query: 217 LGMSLPGCASIPAPYRERGQMAYATGKRICELVLQ-------DIRPSQIMTRQAFENAIA 269 LG+SLPG S+ A + +R ++ G+R+ +L + + P I + +AFENA+A Sbjct: 211 LGLSLPGNGSMLATHADRRELFLEAGRRVMKLAKRYYGDDDASVLPRSIASFKAFENAMA 270 Query: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPA-GKYLGEGFHRAG 328 + A+G SSN HL+A A+ V+ ++DD RI VP L P+ KY E HRAG Sbjct: 271 LDVAMGGSSNTVLHLLAAAQEAEVDFTMDDIDRISRKVPHLCKVAPSTPKYHMEDVHRAG 330 Query: 329 GVPSVMHELQKAGRLHEDCATVSG-----RTIGEIVSSSLTSNADVIHPF---------- 373 GV +++ EL +AG LH D V+ +++ E LT + + +H F Sbjct: 331 GVMAILGELDRAGLLHTDVNHVASEDGTLKSVLERFDVVLTKD-EKVHEFFRAGPAGIPT 389 Query: 374 -------------------------DTPLKHRAGFIVLSGNFFDS-AIMKMSVVGEAFRK 407 + G VLSGN ++ I+K + V E+ K Sbjct: 390 TRAFSQSCRWDTLDDDRREGCIRSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLK 449 Query: 408 TYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVN 467 F A V+E ED A I + + ++VIR G G PG E+ Sbjct: 450 -----------FSGVARVYESQEDAVAGILGGEVVAGD--VVVIRFEGPKGGPGMQEM-- 494 Query: 468 MAPPAALIKQGIDS-LPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLN 526 + P + L +G+ + + DGR SG ++ SI ++SPEAA GG + L++ DR+ +D+ Sbjct: 495 LYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTIGLIENGDRIDIDIP 554 Query: 527 TRTVNLLIDDEEMARRR--------LEWTP 548 R++ LL+ D E+ RR L W P Sbjct: 555 GRSIKLLVSDAELESRRAAMNAKGPLAWKP 584 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: 861 Number of extensions: 46 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: 618 Length adjustment: 37 Effective length of query: 557 Effective length of database: 581 Effective search space: 323617 Effective search space used: 323617 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