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 GFF438 PGA1_c04490 indolepyruvate oxidoreductase
Query= reanno::psRCH2:GFF3452 (1156 letters) >FitnessBrowser__Phaeo:GFF438 Length = 1140 Score = 1036 bits (2679), Expect = 0.0 Identities = 542/1137 (47%), Positives = 737/1137 (64%), Gaps = 11/1137 (0%) Query: 7 RLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWE 66 +LDD+Y G ++LTGTQAL R+ + Q +RD++ GLNT GF+SGYRGSPLGG+D W Sbjct: 12 QLDDRYDYTKGRVFLTGTQALARVMLDQARRDRSAGLNTAGFVSGYRGSPLGGVDLEFWR 71 Query: 67 ARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDVF 126 +R + H I F P VNE+L ATAV G+QQ L P + +GVF+MWYGKGPGVDR+GD Sbjct: 72 SRKRMDAHNITFMPAVNEDLGATAVLGAQQAILDPHCEVEGVFSMWYGKGPGVDRSGDAL 131 Query: 127 KHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIG 186 KH NA G S +GGVL++AGDDHGC SS++PHQS+ AF++ +PVLNPA+V E L +G G Sbjct: 132 KHGNAYGSSEKGGVLVVAGDDHGCVSSSMPHQSDVAFMSWFMPVLNPADVSEFLQFGEYG 191 Query: 187 WELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPLAQE 246 + LSRYSG WV K ++E V+S+ VE+ P R T PE + P G+HIR D P + Sbjct: 192 FALSRYSGTWVGFKAVSETVESARSVELRPDRSFT-YPELPDYP-GGLHIRRSDLPSPEI 249 Query: 247 KRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALCAS 306 + K+ A RAFA AN ++ + D P + G +TTGK +LD+ +AL LGLD+A C Sbjct: 250 ETRIHAKLRAVRAFAEANPIDTRIYDLPKAKFGFVTTGKGHLDLMEALRLLGLDQAACKR 309 Query: 307 VGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRVVG 366 +G+ + KVGM WPL F +G E+LVVEEKR IIE Q Y+WP K R+VG Sbjct: 310 LGIDIYKVGMVWPLARTEALRFVKGKQEVLVVEEKRGIIESQFKEYFYDWPGDKPERMVG 369 Query: 367 EFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYSTV 426 + D QGN L+P EL+P + ++A+RL + +++ R L A+ L +T Sbjct: 370 KHDSQGNPLIPWTGELSPLTLVPIVAERLNRFFPEENLLDRANALTAQPPRLLNVPGAT- 428 Query: 427 RTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQAPFT 486 RTP++CSGCPHN+STK+PEGS+A++GIGCH M WMDR T + QMGGEGV W + F Sbjct: 429 RTPYFCSGCPHNTSTKLPEGSKANSGIGCHVMASWMDRDTAGYAQMGGEGVPWTVASKFN 488 Query: 487 DTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQLS 546 H+FQNLG+GT++HSGSLA+R AVAA N+TYKILYNDAVAMTGGQP+DG + V ++ Sbjct: 489 GGKHVFQNLGEGTWYHSGSLAIRQAVAADTNITYKILYNDAVAMTGGQPVDGPVSVSGIA 548 Query: 547 RQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIYDQT 606 + EGV RIALVSD+ +K+ S+ F TSFH R +LD+VQRELRE GV+V+IY+QT Sbjct: 549 QTCRAEGVDRIALVSDDIEKF-SKSEFPAGTSFHDRSDLDSVQRELREIPGVTVLIYEQT 607 Query: 607 CATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREIDQNA 666 CATEKRRRRKRG MEDP + AFIN CEGCGDC +SNCL+V P ET GRKR+I+ ++ Sbjct: 608 CATEKRRRRKRGTMEDPKRFAFINDLACEGCGDCSVESNCLSVEPKETPFGRKRKINLSS 667 Query: 667 CNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAAT--LPEPQHPTLDRPWNVLIPGVG 724 CNKDFSC+ GFCPSFVTV G RK E A A T LP P P+L P+++L+ GVG Sbjct: 668 CNKDFSCLNGFCPSFVTVEGATRRKKEVAALDASALTADLPSPALPSLKEPFDLLVTGVG 727 Query: 725 GSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIAAGEA 784 G+GV T+GAL+ MAAHLEGKG +VLD G AQKFG V ++R++ ++ VRI A Sbjct: 728 GTGVVTVGALITMAAHLEGKGASVLDFTGFAQKFGTVLGYIRLSNTPEALHQVRIDQSAA 787 Query: 785 DLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAISDAV 844 D ++GCD++V++ ++ + + V+N E T + DA + +I+D + Sbjct: 788 DAVIGCDVVVSSAPKASAHYRDG-TKMVLNRAEMPTGDLVLRRDADLMANLRETSIADVI 846 Query: 845 GADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSAKLNL 904 GAD +A A LLGD++ N+ +LGFA+Q GL+P+S A+++AI LNGV+ + N Sbjct: 847 GADNLSGFNANEAAETLLGDAVLANVMMLGFAWQNGLVPVSLGALDQAIVLNGVAIEKNR 906 Query: 905 QAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRYRQLV 964 AF GR + + L D E +TL E++D R FLT YQ A+ Y L+ Sbjct: 907 LAFAIGRAFAHDPARLSDLYHEADAPE---ETLAELIDRRATFLTGYQDVAYAQSYTALL 963 Query: 965 ERVRDA-DSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYKLQF 1023 E +R+A S AL A AR FKL+AYKDE+EVARL S+ F+ QLEA+F+GD+++ + Sbjct: 964 EVLRNALPSKGSDALVTAAARSLFKLMAYKDEFEVARLLSDDSFKHQLEAEFDGDFRVNY 1023 Query: 1024 HLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVERQLI 1083 HLAP L+++ G P+K + G W+ +LAK R +RG+ +PFG + R+ R L+ Sbjct: 1024 HLAPPLLSRKSDARGRPQKMQFGAWMRPALRLLAKGRRMRGSRWNPFGRHEEARLHRDLL 1083 Query: 1084 SEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQL 1140 + Y+ + ++ + + + P IRGYGPV+ + K + + E L Sbjct: 1084 AWYQTIITRTAEHYSHEHHDGWLKVLSAPMDIRGYGPVRMAAAEKVKAEVSARLETL 1140 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: 2932 Number of extensions: 119 Number of successful extensions: 8 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: 1140 Length adjustment: 46 Effective length of query: 1110 Effective length of database: 1094 Effective search space: 1214340 Effective search space used: 1214340 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