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 3608360 Dshi_1762 pyruvate ferredoxin/flavodoxin oxidoreductase (RefSeq)
Query= reanno::psRCH2:GFF3452 (1156 letters) >FitnessBrowser__Dino:3608360 Length = 1135 Score = 1044 bits (2699), Expect = 0.0 Identities = 557/1131 (49%), Positives = 745/1131 (65%), Gaps = 19/1131 (1%) Query: 1 MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60 MSL +IRL D+Y L + L GTQAL RL ++Q RD+A GLNTGG+++GYRGSPLG + Sbjct: 1 MSLQDIRLSDRYDLDRETVLLNGTQALVRLTLMQAARDRAAGLNTGGYVTGYRGSPLGAV 60 Query: 61 DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120 D+ + D L++ + F+PG+NE+LAATA+WG+QQ L DGVF MWYGKGPGVD Sbjct: 61 DQQMGRNLDLLREAGVIFEPGLNEDLAATALWGTQQAELRGEGSRDGVFGMWYGKGPGVD 120 Query: 121 RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180 R+GDV KHAN AG SP GGVL + GDDH +SST HQSE A + A +PVL+PA VQEIL Sbjct: 121 RSGDVMKHANLAGTSPHGGVLFVMGDDHTGESSTTCHQSEFALLDAYMPVLSPAGVQEIL 180 Query: 181 DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240 DYG+ GW LSRY+G WV LK + + V+++AVV+ R++ P D+ +PE G++IR D Sbjct: 181 DYGLFGWALSRYAGVWVGLKAMKDTVEATAVVDGRADRMRFVTP-DYAMPEGGLNIRLVD 239 Query: 241 PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300 QE+RL +K YAA AF AN +++ ML P ++G + GK++LD+ ALD LG+D Sbjct: 240 HWTPQEERLIAHKRYAAEAFGHANGIDKRMLGKPGAKIGFLAAGKNWLDLAHALDLLGID 299 Query: 301 EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360 A ++G+ KVGM+WPL+ +A+GLD I+VVEEKR ++E Q+ ++N + Sbjct: 300 GARAEALGITAYKVGMTWPLDVKGFLGWAEGLDVIVVVEEKRKLLEVQVKEAIFN--DRR 357 Query: 361 RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPI-YTSDSIQARLAFLAAKEKALA 419 RV G G L P L P IA + + L S+ ++ARLA LA +A Sbjct: 358 GRRVYGGQKAPGEVLFPAYGALDPVTIAEKLGQILIEEGRASEDLEARLARLAEVRRADN 417 Query: 420 ARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNW 479 A+ + RTP++CSGCPHN+ST+VPEG+ A AGIGCH M WMDR T +T MG EG NW Sbjct: 418 AKDLA-ARTPYFCSGCPHNTSTRVPEGAIAYAGIGCHVMAMWMDRDTNGYTHMGAEGANW 476 Query: 480 IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539 IG+ F+ H+FQNLGDGTY HSG A+RAA AA N+TYKIL+NDAVAMTGGQ DG Sbjct: 477 IGEGKFSTRSHVFQNLGDGTYNHSGIQAIRAAHAAKANITYKILFNDAVAMTGGQTNDGG 536 Query: 540 LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599 L +++ ++ G++ I +V DE ++ F P H R EL VQ EL++ +G + Sbjct: 537 LDAARIAWELKGIGLRDIRIVYDEKEEV-DFSAFPPDLPRHGRDELMTVQEELQQVRGTT 595 Query: 600 VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659 I+Y QTCA EKRRRRKRG DP KR FIN VCEGCGDCG +SNC+A++P ETELGRK Sbjct: 596 AILYIQTCAAEKRRRRKRGTFPDPDKRVFINTDVCEGCGDCGVQSNCVAIVPAETELGRK 655 Query: 660 REIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVL 719 R +DQ+ACNKDFSC++GFCPSFVTV G RK A ++ LP+P P +D N+L Sbjct: 656 RAVDQSACNKDFSCLKGFCPSFVTVSGARPRK--AATAEVDLGHLPDPALPAIDGTHNLL 713 Query: 720 IPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRI 779 I GVGG GV T+GA L MAAHLEGKG +++ AGLAQK G V H RIAA+ DI AVR+ Sbjct: 714 ITGVGGMGVVTIGATLAMAAHLEGKGVGMMEMAGLAQKGGAVQIHCRIAARPEDITAVRV 773 Query: 780 AAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQA 839 + GEA ++G DL+V + + + + AVVNSHE T FTR+ + ++PGA ++ + Sbjct: 774 SVGEAHGVIGGDLVVTGAGKIQGMMAKGRTGAVVNSHEIVTGAFTRDREFRIPGADLQVS 833 Query: 840 ISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVS 899 + +GA+ F DA+ LA ++LGD+I +N+ + G A+Q+GL+P+ +AI +AI+LNG + Sbjct: 834 LQARLGAEAVVFFDASELAQKVLGDAIFSNMVVTGAAWQRGLIPLGRDAIFQAIKLNGAA 893 Query: 900 AKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARR 959 N QAF GR AVL EAV ++ P K+L E +D+R D L YQSA LA++ Sbjct: 894 PDRNKQAFDLGRWAVLNPEAVAKMLAAEVTARP--KSLAEKIDFRADHLRAYQSARLAKK 951 Query: 960 YRQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDY 1019 YR+ VE V D D L VA+ Y KLL+YKDEYEV+RL + R + EA FEG+ Sbjct: 952 YRRAVEAVTDPD------LRAVVAQNYHKLLSYKDEYEVSRLLRDT--RAKAEAAFEGEL 1003 Query: 1020 KLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVE 1079 +L +HLAP L++ P G PRKR G W+ +G LA + LRGTPLDPFGY +RR+E Sbjct: 1004 ELTYHLAPPLLSRAGP-DGRPRKRAFGSWIEKAYGPLAALKLLRGTPLDPFGYTAERRME 1062 Query: 1080 RQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKAR 1130 R+LI YE + + A++ P A A+ A P+ +RG+GPVK +++ R Sbjct: 1063 RELIRLYEADLARVQAEMTPARAEAARALLAWPDMVRGFGPVKAQAVETMR 1113 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: 2842 Number of extensions: 121 Number of successful extensions: 9 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: 1135 Length adjustment: 46 Effective length of query: 1110 Effective length of database: 1089 Effective search space: 1208790 Effective search space used: 1208790 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 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