Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 8501745 DvMF_2461 fumarate hydratase (RefSeq)
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Miya:8501745 Length = 279 Score = 186 bits (473), Expect = 7e-52 Identities = 113/283 (39%), Positives = 158/283 (55%), Gaps = 16/283 (5%) Query: 22 LIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEGKRPICQD 81 +++ +A + Y P D A RA E+S AK+ Q+L N+ + A P+CQD Sbjct: 9 VVEEVARLCVECNRYLPKDVRWAFCRAQAEEESDVAKEVFRQLLENADLAATTGLPLCQD 68 Query: 82 TGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEGGRKNTKDN 141 TG+ FV++G D R DG T+ + I EGVR GY + LR S P RKNT DN Sbjct: 69 TGLAVFFVELGEDCRVDGMTL--REAITEGVRIGYA--EGYLRKSACDPMT--RKNTGDN 122 Query: 142 TPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPS---DSIVDWILKTVPTMGAGWC 198 TPAVIH ++VPG+ + + AKGGGSEN S+ ML P+ I D++++ V G C Sbjct: 123 TPAVIHMDLVPGDRLRIAFMAKGGGSENMSRVTMLAPAQGWQGIKDFVVQRVREAGPNPC 182 Query: 199 PPGMLGIGIGGTAEKAMVMAKESLMDPI-DIQDVIARGPKDWIEELRVELHEKVNALGIG 257 PP ++G+G+GGT + A ++AK++L+ P+ DI P + EL +N LGIG Sbjct: 183 PPTIIGVGVGGTFDYAPILAKKALLRPLTDIH------PDPDMAAKEAELLAAINELGIG 236 Query: 258 AQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTL 300 GLGG T L VK+ AP H AS P+A+ C + RH L Sbjct: 237 PMGLGGKTTCLGVKMAFAPCHLASLPLAVNVQCHSVRHGEIEL 279 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: 344 Number of extensions: 17 Number of successful extensions: 4 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: 279 Length adjustment: 30 Effective length of query: 490 Effective length of database: 249 Effective search space: 122010 Effective search space used: 122010 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: 50 (23.9 bits)
Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 8501746 DvMF_2462 hydro-lyase, Fe-S type, tartrate/fumarate subfamily, beta subunit (RefSeq)
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__Miya:8501746 Length = 175 Score = 131 bits (329), Expect = 2e-35 Identities = 73/166 (43%), Positives = 98/166 (59%), Gaps = 1/166 (0%) Query: 336 LTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKGEKLPVDFTNRVIYYVGPVDPV 395 LT E VA G + LSG + T RDAAH+R+A+ L +GE P D VIYYVGP Sbjct: 10 LTDEAVAQLRSGDVVFLSGTIYTARDAAHRRLAESLDRGEDPPFDLRGAVIYYVGPSPAP 69 Query: 396 RDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAERGPVAIEAIRKHKAAYLMAVGGA 455 +G AGPTT+ RMD + + A GL + IGK R +A+++H A YL A GGA Sbjct: 70 PGRPIGSAGPTTSYRMDSYAPRLHA-LGLKATIGKGRRNTEVRDALKQHTAVYLGATGGA 128 Query: 456 AYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAVDSNGTSVH 501 L+S+ I +A V+A++DLG EAI E V+D P+ V D G ++ Sbjct: 129 GALLSQCITAATVIAYDDLGPEAIRELTVKDFPLLVINDCVGGELY 174 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: 256 Number of extensions: 8 Number of successful extensions: 2 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: 175 Length adjustment: 26 Effective length of query: 494 Effective length of database: 149 Effective search space: 73606 Effective search space used: 73606 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: 48 (23.1 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