Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 208788 DVU3264 tartrate dehydratase alpha subunit, putative
Query= BRENDA::Q141Z6 (520 letters) >MicrobesOnline__882:208788 Length = 279 Score = 187 bits (475), Expect = 4e-52 Identities = 111/290 (38%), Positives = 164/290 (56%), Gaps = 14/290 (4%) Query: 14 MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73 M I +D+I+++A +++ P D A RA+ E ++ Q+L N+ + A Sbjct: 1 MRKIPAKDVIEAVARLCTGCNHHLPGDVRAAFERAHAAETDDVPREVFRQLLENADLAAN 60 Query: 74 GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133 P+CQDTG+ FV++G R DG + + + I EGVR+GY + LR S P Sbjct: 61 SALPLCQDTGLAVFFVEMGEGCRVDG--LALREAITEGVRKGY--GEGHLRKSSCDP--F 114 Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSD---SIVDWILKTV 190 R NT DNTPA+IH ++VPG+ + + AKGGGSEN S+ ML P+ I D++++ V Sbjct: 115 SRANTGDNTPAIIHIDLVPGDRLHIAFMAKGGGSENMSRVTMLAPAQGWKGIRDFVVRRV 174 Query: 191 PTMGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEK 250 G CPP ++G+G+GGT E A +++K++L+ +D DV P + EL + Sbjct: 175 AEAGPNPCPPVLVGVGVGGTFEYAAMLSKKALLRNVD--DV---HPDAALAAREAELLDA 229 Query: 251 VNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTL 300 +NALGIG GLGG T L VK+ AP H AS P+A+ C + RH TL Sbjct: 230 INALGIGPMGLGGRTTCLAVKMAVAPCHLASLPLAVNIQCHSARHGEVTL 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: 320 Number of extensions: 13 Number of successful extensions: 5 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 208789 DVU3265 tartrate dehydratase beta subunit, putative
Query= BRENDA::Q141Z6 (520 letters) >MicrobesOnline__882:208789 Length = 183 Score = 132 bits (333), Expect = 8e-36 Identities = 73/168 (43%), Positives = 100/168 (59%), Gaps = 1/168 (0%) Query: 336 LTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKGEKLPVDFTNRVIYYVGPVDPV 395 LT V A G +LLSG + T RDAAH+R+ D L +GE+ P D VIYYVGP Sbjct: 10 LTDTAVDALRSGDVILLSGTIYTARDAAHRRLCDALDRGEQPPFDLRGAVIYYVGPSPAP 69 Query: 396 RDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAERGPVAIEAIRKHKAAYLMAVGGA 455 +G AGPTT+ RMD + + A GL + IGK R +A+ +H A Y A GGA Sbjct: 70 PGHPIGAAGPTTSYRMDSYAPRLHA-LGLKATIGKGRRHATVRKALSEHTAVYFGATGGA 128 Query: 456 AYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAVDSNGTSVHQT 503 L+++ I +A+V+A++DLG EAI E VQD P+ V D++G ++ T Sbjct: 129 GALLAQRITAARVIAYDDLGPEAIRELTVQDFPLLVINDAHGGELYVT 176 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: 269 Number of extensions: 5 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: 183 Length adjustment: 27 Effective length of query: 493 Effective length of database: 156 Effective search space: 76908 Effective search space used: 76908 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