Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 1937120 b3771 dihydroxy-acid dehydratase (NCBI)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Keio:1937120 Length = 616 Score = 192 bits (489), Expect = 3e-53 Identities = 166/565 (29%), Positives = 263/565 (46%), Gaps = 77/565 (13%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 GMT + G+PII + + + P + H +L + V I AGG+ EF + + Sbjct: 26 GMTDADF--GKPIIAVVNSFTQFVPGHVHLRDLGKLVAEQIEAAGGVAKEFNTIAVDDGI 83 Query: 95 RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 + R L + +++ + D +V + CDK TP LMA+ ++P I + Sbjct: 84 AMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPVIFV 143 Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAG---EIDYEGFMEMTTAASPSVGHCNTMGT 206 SGGPM G K + + + M G ++ ++ +A P+ G C+ M T Sbjct: 144 SGGPMEAGKTK---LSDQIIKLDLVDAMIQGADPKVSDSQSDQVERSACPTCGSCSGMFT 200 Query: 207 ALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVR-------QDIRPSQIM 259 A SMN L EALG+S PG S+ A + +R Q+ GKRI +L + + P I Sbjct: 201 ANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIVELTKRYYEQNDESALPRNIA 260 Query: 260 TRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPA-GK 318 ++ AFENA+ + A+G S+N HL+A A+ ++ ++ D ++ VP L P+ K Sbjct: 261 SKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSDIDKLSRKVPQLCKVAPSTQK 320 Query: 319 YLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSN---SLTSNTDVIHPF-- 373 Y E HRAGGV ++ EL +AG L+ D V G T+ + + LT + V + F Sbjct: 321 YHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQTLEQYDVMLTQDDAVKNMFRA 380 Query: 374 -----------------DT-----------PLKHR----AGFIVLSGNFFDS-AIMKMSV 400 DT L+H G VL GNF ++ I+K + Sbjct: 381 GPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDGGLAVLYGNFAENGCIVKTAG 440 Query: 401 VGEAFRKTYLSEPGAENSFEARAIVFEGPED-YHARIDDPALDIDERCILVIRGVGTVGY 459 V ++ K F A V+E +D A + + D ++VIR G G Sbjct: 441 VDDSILK-----------FTGPAKVYESQDDAVEAILGGKVVAGD---VVVIRYEGPKGG 486 Query: 460 PGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTN 518 PG E+ + P + L G+ + + DGR SG ++ SI ++SPEAA GG + L++ Sbjct: 487 PGMQEM--LYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGLIEDG 544 Query: 519 DRLKVDLNTRTVNLLIDDAEMAQRR 543 D + +D+ R + L + DAE+A RR Sbjct: 545 DLIAIDIPNRGIQLQVSDAELAARR 569 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: 801 Number of extensions: 39 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