Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate AO356_13250 AO356_13250 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_13250 Length = 613 Score = 213 bits (543), Expect = 1e-59 Identities = 169/553 (30%), Positives = 255/553 (46%), Gaps = 69/553 (12%) Query: 45 RPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAAL--- 101 +PII IA + + P + H +L Q V I GG+ EF + + + Sbjct: 34 KPIIAIANSFTQFVPGHVHLKDLGQLVAREIERVGGVAKEFNTIAVDDGIAMGHDGMLYS 93 Query: 102 --DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHH 159 R + + +++ + D +V + CDK TP LMAA ++P I +SGGPM G Sbjct: 94 LPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFVSGGPMEAG-- 151 Query: 160 KGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGM 219 K +L G L A + A E E +A P+ G C+ M TA SMN L EALG+ Sbjct: 152 KTKLASHGLDLVDAMVIAADSSASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGL 211 Query: 220 SLPGCASIPAPYRERGQMAYATGKRICDLVR-------QDIRPSQIMTRQAFENAIAVAS 272 +LPG S A + +R Q+ G+ I +L + + + P I +AFENA+ + Sbjct: 212 ALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGENDESVLPRNIANFKAFENAMTLDI 271 Query: 273 ALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMP-AGKYLGEGFHRAGGVP 331 A+G S+N HL+A A+ ++ L D R+ VP L P KY E HRAGG+ Sbjct: 272 AMGGSTNTILHLLAAAQEAEIDFDLRDIDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIF 331 Query: 332 SVMHELQKAGRLHEDCATVSGKTIGEIVSN-SLTSNTD-VIHPF---------------- 373 S++ L + G LH D TV K++ E ++ +T TD +H F Sbjct: 332 SILGSLARGGLLHTDLPTVHSKSMAEAIAKWDITQTTDEAVHHFFKAGPAGIPTQTAFSQ 391 Query: 374 -------------------DTPLKHRAGFIVLSGNF-FDSAIMKMSVVGEAFRKTYLSEP 413 + G VL GN D ++K + V E+ Sbjct: 392 STRWDTLDDDRENGCIRSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESI-------- 443 Query: 414 GAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAA 473 + FE A +FE + I A ++ I++IR G G PG E+ + P + Sbjct: 444 ---HVFEGNAKIFESQDSAVRGI--LADEVKAGDIVIIRYEGPKGGPGMQEM--LYPTSY 496 Query: 474 LIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNL 532 L +G+ + L DGR SG ++ SI + SPEAA GG + L++ D++ +D+ R++NL Sbjct: 497 LKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGDKVLIDIPNRSINL 556 Query: 533 LIDDAEMAQRRRE 545 LI D E+A RR E Sbjct: 557 LISDEELAGRRIE 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: 861 Number of extensions: 34 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: 613 Length adjustment: 37 Effective length of query: 557 Effective length of database: 576 Effective search space: 320832 Effective search space used: 320832 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