Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate RR42_RS10350 RR42_RS10350 indolepyruvate ferredoxin oxidoreductase
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__Cup4G11:RR42_RS10350 Length = 1162 Score = 1004 bits (2597), Expect = 0.0 Identities = 549/1177 (46%), Positives = 735/1177 (62%), Gaps = 59/1177 (5%) Query: 22 LEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWKA 81 LED+Y E G V+++GTQALVR+ + Q DR AGL T G +SGYRGSPLG DQ LW+ Sbjct: 7 LEDRYRREAGSVFLTGTQALVRILVEQARADRIAGLKTGGLVSGYRGSPLGGFDQELWRQ 66 Query: 82 KQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVFK 141 + LA ++I F+ GLNEDL AT +WG+QQ++ +P R EGVF MWYGKGPGVDRT DVF+ Sbjct: 67 RSLLAEYEIRFEPGLNEDLGATMLWGAQQIDAFPGKRVEGVFSMWYGKGPGVDRTGDVFR 126 Query: 142 HANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHAW 201 +AN G+SRHGGVL +AGDDHAA+SS HQ++H+F+ +PVL+P++V+EY+++GL + Sbjct: 127 NANVLGTSRHGGVLAIAGDDHAAQSSMFPHQTDHVFEGAMMPVLFPASVEEYVEFGLFGY 186 Query: 202 AMSRYSGLWVSMKCVTDVVESSASVEL----DPHRVEIVLPQDFILPPGGLN----IRWP 253 A+SR+SGLWV+ K +T+ VES S+ + LP D +P G ++WP Sbjct: 187 ALSRFSGLWVAFKAITETVESGRSMLIGGAGSARGARFSLPGDIDIPERGFGYDTGVKWP 246 Query: 254 DPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGL 313 E E RLL+ + A A+ RAN IDR + AR GI+T GKA+ D ALA LGL Sbjct: 247 GQRAELERRLLEERLPAAQAFARANPIDRTIVRPRDARIGIVTVGKAHGDLLAALARLGL 306 Query: 314 DDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDD 373 D+ A +GI LYK+G WP+E G R FA G++ +LVVEEKR +E ++E L+N Sbjct: 307 DEPRLAELGIGLYKIGMTWPIEGEGVRRFASGMRALLVVEEKRSFVERQIQETLFNVAAP 366 Query: 374 VRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARI 433 RP+V+GK D LLPA E +P + +A L +F V A Sbjct: 367 QRPEVFGKRGPNDAP-----------LLPATLEFAPDQLQKA----LRQFLAYTGVHALP 411 Query: 434 AARIAVIEAKEKAMAVPRVAAE-------RKPWFCSGCPHNTSTNVPEGSRALAGIGCHY 486 A + V ++A+ RKP+FC+GCPHN+ST +P+GS A AGIGCH Sbjct: 412 PGNTGSAAALPRQPRVIPLSAQLQPDVLTRKPFFCAGCPHNSSTKLPDGSYAAAGIGCHI 471 Query: 487 MTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVN 546 M + +T+TF QMGGEGV W+G + F+ H+F NLGDGTY HSG LAIR ++AAG Sbjct: 472 MALGQGDNTATFCQMGGEGVQWVGLSSFSDLPHLFVNLGDGTYQHSGSLAIRQAVAAGTA 531 Query: 547 ITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGV 606 +TYKIL+NDAVAMTGGQP +G L+V + Q+ AEG K+V+V+D P++Y A +P V Sbjct: 532 VTYKILFNDAVAMTGGQPTEGGLTVPRMVAQLIAEGVGKVVLVSDHPQRYWGAKSIPASV 591 Query: 607 EVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGC 666 E+ HRD LD +QR LR G + ++YDQTCA EKRRRRKRGT DP +R IN +VCEGC Sbjct: 592 EIAHRDALDDVQRRLRAYRGVSAIVYDQTCAAEKRRRRKRGTLADPVRRVVINPSVCEGC 651 Query: 667 GDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGV 726 GDCSV+SNC+++EPLET LG KR +NQSSCNKD SC+ GFCPSFVT EG Q K+ + + Sbjct: 652 GDCSVQSNCIAIEPLETPLGRKRAVNQSSCNKDMSCLKGFCPSFVTIEGLQPKRANQRRI 711 Query: 727 SMDNL---PALPQPALPG-----LEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTV 778 +LP PA P LEH +LVTGVGGTGVVT+G +L MAAHLE KG Sbjct: 712 QQMEAQWRASLPPPAGPAALGALLEHA-RILVTGVGGTGVVTVGAILAMAAHLEGKGAAT 770 Query: 779 LDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGR 838 LD GLAQK GAV+SHVQ+A +++ RI AD++IGCDA+V+A DV+++ + Sbjct: 771 LDFTGLAQKNGAVVSHVQLADRRERIVTARIEACSADVMIGCDAVVAASPDVLARLRKCG 830 Query: 839 TRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEA-CDFINASGLAVALIGDAIFT 897 TRA+VN+A PTA+F+ N + + + VG +F + + A+ L GDAI T Sbjct: 831 TRAVVNSAVAPTADFVANGDLPISREIHQAAIESVVGAGQAEFFDCTAAAMTLFGDAIAT 890 Query: 898 NPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLR 957 N +++G+A+Q+GW+PLS A+ RAIELNG AVE N+ AF WGR +A +P LR Sbjct: 891 NMMLVGHAYQRGWIPLSEMAIARAIELNGAAVELNRRAFLWGRILACEP-------NALR 943 Query: 958 NTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNG 1017 T+ P L + +A R L+AYQ+AAYA+ + V+ V AE + G Sbjct: 944 RTSAAEAQAAQPFE----LARFVAERKRDLSAYQNAAYAERYGRMVAAVAGAEQRIAGEA 999 Query: 1018 KPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPL 1077 L EA AR+ +++AYKDEYEVARL++DP F L + F+G + F +APP Sbjct: 1000 G--LLAEAVARSYYRVLAYKDEYEVARLHSDPAFARSLESTFDGHGKK----TFHMAPPW 1053 Query: 1078 MAKRDEK-GHLVKRRFGPSTMK-LFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRA 1135 + + D G K + M L +L K LRG FD FG+ ++RR ER +I E Sbjct: 1054 LTRVDRNTGRRNKIVLSGTVMSPLLRLLRHGKILRGTPFDPFGRQSDRRIERRMIVECED 1113 Query: 1136 LLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDN 1172 ++ + R LS A+A L IRGFG +K+ N Sbjct: 1114 DVQLVLRTLSERTLASAAALVGAYAQIRGFGVIKERN 1150 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: 3135 Number of extensions: 144 Number of successful extensions: 10 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: 1162 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1115 Effective search space: 1282250 Effective search space used: 1282250 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: 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