Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate Dsui_0379 Dsui_0379 indolepyruvate ferredoxin oxidreductase, alpha/beta subunit
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__PS:Dsui_0379 Length = 1183 Score = 1429 bits (3698), Expect = 0.0 Identities = 724/1186 (61%), Positives = 882/1186 (74%), Gaps = 32/1186 (2%) Query: 13 IRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLG 72 + + LA+ SL+DKYT GR +++GTQAL+RLPMLQR RD+A GLNTAGFISGYRGSPLG Sbjct: 8 VPKELASASLDDKYTTLSGRAFLTGTQALIRLPMLQRLRDQAQGLNTAGFISGYRGSPLG 67 Query: 73 ALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPG 132 LDQ LWKA+++LA + I FQ G+NEDLAAT+VWGSQQVN++P A+++GVF +WYGKGPG Sbjct: 68 GLDQGLWKAQKYLAENHITFQPGVNEDLAATAVWGSQQVNLFPGAKYDGVFALWYGKGPG 127 Query: 133 VDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQE 192 VDR+ DVF+HAN+AGSSRHGGVLV+AGDDHAAKSSTL HQ+EH+FKA +PVLYP+NVQE Sbjct: 128 VDRSGDVFRHANAAGSSRHGGVLVVAGDDHAAKSSTLPHQTEHVFKAVMMPVLYPANVQE 187 Query: 193 YLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRW 252 YL+YGLH WAMSRYSG WV+ K + D VE+SASV +DP ++I LP DF LP GLNIRW Sbjct: 188 YLEYGLHGWAMSRYSGCWVAFKALADTVETSASVWVDPMALDIRLPDDFELPADGLNIRW 247 Query: 253 PDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLG 312 PDPPL QEARL +K YA LAY RAN+++RI IDSP R GI+T GK+YLD QAL LG Sbjct: 248 PDPPLVQEARLTHFKLYAALAYARANRLNRIVIDSPAPRLGIITAGKSYLDVMQALDELG 307 Query: 313 LDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRD 372 +D + A+IGIRLYKVG VWPLE+ G R FAEGL EILVVEEKRQ++EY LKEELYNWR+ Sbjct: 308 IDQQLAAQIGIRLYKVGMVWPLESEGVRQFAEGLDEILVVEEKRQMLEYQLKEELYNWRE 367 Query: 373 DVRPKVYGKFDEKDNAGGEWSI--------PQSNWLLPAHYELSPAIIARAIATRLDK-F 423 DVRP+V GKFDEK GEW++ +WLLPA ELS A IARAIA+R+++ F Sbjct: 368 DVRPRVVGKFDEK----GEWALLPDGKGHLAHGDWLLPAAGELSVAQIARAIASRIERHF 423 Query: 424 ELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIG 483 PA I AR+ +IEAK+KA+ P + +R P FCSGCPHNTST VPEGSRA+AGIG Sbjct: 424 TSPA-----IKARLDLIEAKQKALQTPLILTQRTPHFCSGCPHNTSTRVPEGSRAVAGIG 478 Query: 484 CHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAA 543 CHYM WMDRSTSTF+ MGGEGV W+GQAPF +KH+FANLGDGTYFHSGLLAIR S+AA Sbjct: 479 CHYMVTWMDRSTSTFTHMGGEGVTWVGQAPFTEEKHIFANLGDGTYFHSGLLAIRQSVAA 538 Query: 544 GVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLP 603 NITYKILYNDAVAMTGGQP+DG LSV + Q+ AEG ++V+VTDEPEKY+ L Sbjct: 539 KTNITYKILYNDAVAMTGGQPVDGILSVPRITRQLEAEGVGRMVIVTDEPEKYAEVTDLA 598 Query: 604 QGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVC 663 V V HRDELD +QRELRE+PG TILIYDQTCATEKRRRRKRG D +R FIN+AVC Sbjct: 599 PNVPVRHRDELDAVQRELREIPGTTILIYDQTCATEKRRRRKRGKLADVDRRVFINEAVC 658 Query: 664 EGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPER 723 EGCGDCSV+SNCLSV P+ET+ G KR I+QS+CNKDFSC+ GFCPSFVT EGA++KK + Sbjct: 659 EGCGDCSVQSNCLSVIPVETDFGRKRAIDQSNCNKDFSCLKGFCPSFVTLEGAKLKKGQA 718 Query: 724 HGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAG 783 + + P LP+P LP PY +LVTGVGGTGVVT+G L+GMAAHL+ KGV+VLDM G Sbjct: 719 LAMDAQDWPPLPEPVLPPTARPYNLLVTGVGGTGVVTLGALIGMAAHLDGKGVSVLDMTG 778 Query: 784 LAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIV 843 LAQK GAV +H++ A P+ +HA RIA GEAD ++G D +V+A ++ +SK GRTRA+V Sbjct: 779 LAQKYGAVFTHLRFADRPEDIHAARIATGEADAILGGDVVVTAGNEALSKMLEGRTRAVV 838 Query: 844 NTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFTNPLVL 902 N +TPTAEF +NP WQFP +Q V VG + F++A LA AL+GDA++TN +L Sbjct: 839 NCTETPTAEFTRNPDWQFPLARMQQTVTATVGADHAWFLDAQALATALMGDALYTNMFLL 898 Query: 903 GYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEG 962 GYAWQKG +P+SL AL RAIELNGTAV N A DWGR A D V L +T Sbjct: 899 GYAWQKGLVPVSLPALGRAIELNGTAVAANLQALDWGRRAAVDEARVRQLATPAADTP-- 956 Query: 963 AEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPL 1022 P A LE+++A R + LT YQDAA A+ +R + +R AE+ L LP+ Sbjct: 957 ------PPRPDAALEEVLALREQELTDYQDAALARRYRQRIEALRQAEAPL---DPALPV 1007 Query: 1023 TEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRD 1082 T AAARN K++A KDEYEVARL+T P F +LR F GEPG+DY ++ LAPPL A+ D Sbjct: 1008 TLAAARNYFKVLAIKDEYEVARLHTRPEFFARLRQTFAGEPGKDYAVHVHLAPPLWARPD 1067 Query: 1083 EK-GHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELT 1141 + G + KR++GP + +LA+LK LRG DVFG TAERR ERAL Y A LE + Sbjct: 1068 PRSGQIRKRQYGPWMLGALKLLARLKFLRGTALDVFGHTAERRMERALQAGYEADLERIL 1127 Query: 1142 RGLSAAN-HATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQ 1186 L+A + H + LA LP+ +RG+GHVK + K R + LL + Sbjct: 1128 EALAAGSAHPALLELARLPESVRGYGHVKAASAEKARQQRQELLRK 1173 Lambda K H 0.319 0.135 0.407 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: 3365 Number of extensions: 135 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: 1197 Length of database: 1183 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1136 Effective search space: 1306400 Effective search space used: 1306400 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 (21.7 bits) S2: 59 (27.3 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