Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate Ga0059261_3334 Ga0059261_3334 hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region/hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Korea:Ga0059261_3334 Length = 507 Score = 710 bits (1833), Expect = 0.0 Identities = 351/502 (69%), Positives = 417/502 (83%), Gaps = 3/502 (0%) Query: 14 MTV-IKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCA 72 MTV IK DLI S+AD+LQ+ISYYHP+DYI+ALG AY EQSPAAKDAIAQILTNSRMCA Sbjct: 1 MTVTIKAADLIDSVADALQFISYYHPMDYIRALGEAYTAEQSPAAKDAIAQILTNSRMCA 60 Query: 73 EGKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPE 132 EG RPICQDTGIV VFVK GMD R D + + ++++EGVRR YLNP+N LRAS+++ P Sbjct: 61 EGHRPICQDTGIVNVFVKWGMDCRLDDTSRSLQEVVDEGVRRAYLNPENKLRASVLADPA 120 Query: 133 GGRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPT 192 R+NT+DNTP V+H E+V G+ V + VAAKGGGSENKSKF M+NPSDSIVDW+++ +P Sbjct: 121 FTRRNTRDNTPCVLHVEMVAGDKVHIDVAAKGGGSENKSKFKMMNPSDSIVDWVIEMLPQ 180 Query: 193 MGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVN 252 MGAGWCPPGMLGIGIGGTAE +++AK++LM+ ID+ + RGP++ IE+LR+E+ +KVN Sbjct: 181 MGAGWCPPGMLGIGIGGTAEHCVLLAKKALMEQIDMATLKERGPRNDIEKLRIEIFDKVN 240 Query: 253 ALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPS 312 ALGIGAQGLGGLAT+LDVKIM AP HAA KPVA+IPNCAATRHAHFTLDGSG A LEAP Sbjct: 241 ALGIGAQGLGGLATILDVKIMDAPCHAAGKPVAMIPNCAATRHAHFTLDGSGPAYLEAPK 300 Query: 313 LDAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLA 372 LD WP V+W PD + + RVDL+ LTPE V +W G LLL+GKMLTGRDAAHKRIADMLA Sbjct: 301 LDEWPDVNWTPD-KAAIRVDLDALTPEVVQSWKQGDRLLLNGKMLTGRDAAHKRIADMLA 359 Query: 373 KGEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAE 432 GE+LPV+F RVIYYVGPVDPV +E VGPAGPTTATRMDKF MML Q GL++ +GKAE Sbjct: 360 AGEELPVEFKGRVIYYVGPVDPVGEEVVGPAGPTTATRMDKFMRMMLDQ-GLLACVGKAE 418 Query: 433 RGPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVA 492 RGP A +AIR K+AYLMAVGGAAYLV++AI+ +KV+ FEDLGMEAIYEF+VQD PVTVA Sbjct: 419 RGPAATDAIRDAKSAYLMAVGGAAYLVARAIKGSKVVGFEDLGMEAIYEFEVQDFPVTVA 478 Query: 493 VDSNGTSVHQTGPKEWQARIGK 514 VD+ G +VHQ P W+ +I K Sbjct: 479 VDAEGNNVHQLAPLVWKEKIAK 500 Lambda K H 0.316 0.133 0.392 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: 844 Number of extensions: 26 Number of successful extensions: 3 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: 520 Length of database: 507 Length adjustment: 35 Effective length of query: 485 Effective length of database: 472 Effective search space: 228920 Effective search space used: 228920 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 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