Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate Ac3H11_941 Fumarate hydratase class I, aerobic (EC 4.2.1.2)
Query= BRENDA::Q141Z6 (520 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_941 Length = 525 Score = 776 bits (2003), Expect = 0.0 Identities = 388/512 (75%), Positives = 435/512 (84%), Gaps = 11/512 (2%) Query: 12 LAMTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMC 71 + T I+QEDLI+SIA +LQYISYYHP DYI L RAYE E+SPAAKDAIAQILTNS+M Sbjct: 1 MTTTTIRQEDLIESIAGALQYISYYHPTDYIAHLARAYEREKSPAAKDAIAQILTNSKMS 60 Query: 72 AEGKRPICQDTGIVTVFVKVGMDVRWDGATMGVT-------DMINEGVRRGYLNPDNVLR 124 A G+RPICQDTGIV VF+KVGMDVRW+G GV D INEGVRRGY +PDN LR Sbjct: 61 ATGQRPICQDTGIVNVFLKVGMDVRWEGFDAGVDGKPCSLDDAINEGVRRGYNHPDNTLR 120 Query: 125 ASIVSPPEGGRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVD 184 AS+V+ P+ RKNTKDNTPAVI EIVPGNTVD+ VAAKGGGSENKSK MLNP D++VD Sbjct: 121 ASVVADPQFARKNTKDNTPAVIFTEIVPGNTVDITVAAKGGGSENKSKMYMLNPGDNVVD 180 Query: 185 WILKTVPTMGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPK----DWI 240 W+LKTVPTMGAGWCPPGMLGIGIGGTAEKA++MAKESLMD +D+ ++ A+ D + Sbjct: 181 WVLKTVPTMGAGWCPPGMLGIGIGGTAEKAVLMAKESLMDDLDMYELQAKQASGAELDNV 240 Query: 241 EELRVELHEKVNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTL 300 E+LR+EL EKVNALGIGAQGLGGL TVLDVKI PTHAASKP+A+IPNCAATRHAHF + Sbjct: 241 EKLRLELFEKVNALGIGAQGLGGLTTVLDVKIKMYPTHAASKPIAMIPNCAATRHAHFVM 300 Query: 301 DGSGAARLEAPSLDAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGR 360 DGSG L PSLD WP V W PD KSK+V+L+TLT EEVA+W PG TLLL+GKMLTGR Sbjct: 301 DGSGPVYLTPPSLDLWPNVDWAPDYNKSKKVNLDTLTKEEVASWKPGDTLLLNGKMLTGR 360 Query: 361 DAAHKRIADMLAKGEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLA 420 DAAHKRI DMLAKGEKLPVDFTNR+IYYVGPVDPV+ EAVGPAGPTTATRMD FTEMMLA Sbjct: 361 DAAHKRIQDMLAKGEKLPVDFTNRIIYYVGPVDPVKGEAVGPAGPTTATRMDGFTEMMLA 420 Query: 421 QTGLISMIGKAERGPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIY 480 QTGLI+M+GKAERGPVAIEAI+KH++AYLMAVGGAAYLVSKAI++A+V+ F DLGMEAIY Sbjct: 421 QTGLIAMVGKAERGPVAIEAIKKHQSAYLMAVGGAAYLVSKAIKTAQVVGFADLGMEAIY 480 Query: 481 EFDVQDMPVTVAVDSNGTSVHQTGPKEWQARI 512 EFDV DMPVTVAVD+ GTS H TGP EWQ RI Sbjct: 481 EFDVVDMPVTVAVDAGGTSAHITGPAEWQKRI 512 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: 937 Number of extensions: 30 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: 525 Length adjustment: 35 Effective length of query: 485 Effective length of database: 490 Effective search space: 237650 Effective search space used: 237650 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