Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_090447429.1 BLS63_RS19365 indolepyruvate ferredoxin oxidoreductase
Query= reanno::psRCH2:GFF3452 (1156 letters) >NCBI__GCF_900100495.1:WP_090447429.1 Length = 1155 Score = 1897 bits (4915), Expect = 0.0 Identities = 930/1156 (80%), Positives = 1033/1156 (89%), Gaps = 1/1156 (0%) Query: 1 MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60 MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQ QRD A GLNT FISGYRGSPLG L Sbjct: 1 MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQKQRDTAHGLNTACFISGYRGSPLGNL 60 Query: 61 DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120 DKSLWEA+ +L+++ IHFQPGVNEELAATAVWGSQQT+LFPGA+YDGVF+MWYGKGPGVD Sbjct: 61 DKSLWEAKSFLQENHIHFQPGVNEELAATAVWGSQQTSLFPGARYDGVFSMWYGKGPGVD 120 Query: 121 RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180 R GDVFKH N+AGVS GGVLLLAGDDHGCKSS++ +QSEHAFIAASIPVLNPANVQEIL Sbjct: 121 RCGDVFKHGNSAGVSAHGGVLLLAGDDHGCKSSSIANQSEHAFIAASIPVLNPANVQEIL 180 Query: 181 DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240 DYGIIGWELSRYSGCWVALKTIAENVDSSAVV+VDPLRV ++PEDFELP DGVHIRWPD Sbjct: 181 DYGIIGWELSRYSGCWVALKTIAENVDSSAVVDVDPLRVDVKLPEDFELPADGVHIRWPD 240 Query: 241 PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300 PPL QEKRLN+YKIYAARAFARAN+LN+VMLDSPNPRLGIITTGKSYLDVRQAL+DLGLD Sbjct: 241 PPLVQEKRLNMYKIYAARAFARANDLNKVMLDSPNPRLGIITTGKSYLDVRQALEDLGLD 300 Query: 301 EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360 E LCA VGLRVLKVGMSWPLEPVSVHEFA+GLDEILVVEEKRSIIEDQLTGQLYNWPV K Sbjct: 301 EELCARVGLRVLKVGMSWPLEPVSVHEFAEGLDEILVVEEKRSIIEDQLTGQLYNWPVGK 360 Query: 361 RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420 RPRVVGEFDE G SLLPNLSELTPAMIAR IAKRLAPIY+S SI RLAFLAAKE +LAA Sbjct: 361 RPRVVGEFDETGVSLLPNLSELTPAMIARAIAKRLAPIYSSASIDERLAFLAAKEASLAA 420 Query: 421 RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI 480 +ST+RTPH+CSGCPHNSSTK+PEGSRA GIGCHYM QWMDR T+TFTQMGGEG WI Sbjct: 421 PKHSTLRTPHFCSGCPHNSSTKLPEGSRAQGGIGCHYMTQWMDRNTDTFTQMGGEGATWI 480 Query: 481 GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540 GQAPFTDT H+FQNLGDGTYFHSG LA+RAAVAAGVN+TYKILYNDAVAMTGGQPIDGEL Sbjct: 481 GQAPFTDTAHIFQNLGDGTYFHSGQLALRAAVAAGVNITYKILYNDAVAMTGGQPIDGEL 540 Query: 541 RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSV 600 RVDQLS+Q+F EGVKRIALVSDEP+KYPSR TFAPI SFHHR ELDAVQRELREFKG SV Sbjct: 541 RVDQLSQQVFAEGVKRIALVSDEPEKYPSRATFAPIVSFHHRSELDAVQRELREFKGCSV 600 Query: 601 IIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKR 660 +IYDQTCATEKRRRRKRGK+ DPAKRAFINPAVCEGCGDC KSNCL+VLPLETELGRKR Sbjct: 601 LIYDQTCATEKRRRRKRGKLVDPAKRAFINPAVCEGCGDCSVKSNCLSVLPLETELGRKR 660 Query: 661 EIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLI 720 EIDQNACNKDFSCVEGFCPSFVTVHGG LRKPEAV LPEP+ P+L+RPWN+L+ Sbjct: 661 EIDQNACNKDFSCVEGFCPSFVTVHGGSLRKPEAVGQNALFEVLPEPRQPSLERPWNILL 720 Query: 721 PGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIA 780 PGVGGSGVTT+GALLGMAAHLEGKGC+VLDQAGLAQKFGPV TH+R+AA+Q DIYAVRIA Sbjct: 721 PGVGGSGVTTVGALLGMAAHLEGKGCSVLDQAGLAQKFGPVVTHIRVAAQQDDIYAVRIA 780 Query: 781 AGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAI 840 AGE DLLLGCDL+V+A +E+L +LN++I++AV+NSHE+ATAEFTRNPDAQVPGAAMR+A+ Sbjct: 781 AGETDLLLGCDLVVSASEEALAKLNDKIAHAVINSHEAATAEFTRNPDAQVPGAAMREAL 840 Query: 841 SDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSA 900 +AVGA KTHFVDATRLATRLLGDSIA+NLF+LGFAYQ+GL+P+SAEAI KAIELNGV+ Sbjct: 841 IEAVGAGKTHFVDATRLATRLLGDSIASNLFMLGFAYQKGLVPVSAEAIAKAIELNGVAV 900 Query: 901 KLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRY 960 +LN QAF WGRRA + AVE+LA P P C+TLE+IV RV LT YQ+A A RY Sbjct: 901 QLNQQAFLWGRRAAHDLAAVEKLAAPKVAEAPRCQTLEQIVADRVARLTAYQNAAYAERY 960 Query: 961 RQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYK 1020 R+LV RV AD D ALS+AVARYYFKLLAYKDEYEVARLYS+ F QQLEAQF+GDY+ Sbjct: 961 RELVARVSRADQGTDQALSRAVARYYFKLLAYKDEYEVARLYSDGSFIQQLEAQFQGDYR 1020 Query: 1021 LQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVER 1080 LQFHLAP+WL+K D TG+PRKR+ GPW+L FG+L+KF+FLRGTPLDPFGY +RR+ER Sbjct: 1021 LQFHLAPSWLSKPDAKTGQPRKRQFGPWMLKAFGLLSKFKFLRGTPLDPFGYSAERRLER 1080 Query: 1081 QLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQL 1140 +LI +YE +V LL +L NYR+AVA+A LPEQIRGYG VK+ ++AK R+Q L+ +L Sbjct: 1081 ELIEDYEDSVGHLLKELNAGNYRSAVALAELPEQIRGYGHVKDAAVAKTREQAAQLKARL 1140 Query: 1141 AKGDEVQSVRLFQPAA 1156 E+Q+V+LF+PAA Sbjct: 1141 LV-SEIQAVQLFEPAA 1155 Lambda K H 0.319 0.136 0.405 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: 3290 Number of extensions: 109 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: 1156 Length of database: 1155 Length adjustment: 47 Effective length of query: 1109 Effective length of database: 1108 Effective search space: 1228772 Effective search space used: 1228772 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 (21.8 bits) S2: 58 (26.9 bits)
This GapMind analysis is from Sep 24 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