Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate H281DRAFT_06130 H281DRAFT_06130 indolepyruvate ferredoxin oxidoreductase
Query= reanno::Marino:GFF880 (1172 letters) >FitnessBrowser__Burk376:H281DRAFT_06130 Length = 1176 Score = 981 bits (2535), Expect = 0.0 Identities = 546/1178 (46%), Positives = 735/1178 (62%), Gaps = 37/1178 (3%) Query: 5 TPQLD-----DYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRG 59 TP+++ DY+LEDRYLRE G VFLTGTQALVRI QA DR+ G+ +AGLVSGYRG Sbjct: 5 TPEVERAIDHDYRLEDRYLREEGTVFLTGTQALVRILFEQARSDRRLGIKSAGLVSGYRG 64 Query: 60 SPLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYG 119 SPLG DQ LW+ K LL + I F P +NEDL AT++ G QQ++ ++V+GVF +WYG Sbjct: 65 SPLGGFDQELWRRKKLLKDADIRFEPGLNEDLGATMVWGAQQIDAFPGKRVDGVFAMWYG 124 Query: 120 KGPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPA 179 KGPGVDR GD ++ G+S GGVL VAGDDH SS PHQ+D F MP I PA Sbjct: 125 KGPGVDRTGDVFRNANILGTSARGGVLAVAGDDHAAQSSMFPHQTDHVFEGAMMPIIFPA 184 Query: 180 NIAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPA----PDFVTPDDFTAPE 235 ++ EY++FGL GYA+SR+SG WV +KAI+ETVES S+ + + F+TP D P Sbjct: 185 SVEEYVKFGLAGYAMSRFSGLWVAYKAITETVESGRSMVVGRSDRANAGFLTPSDVEVPA 244 Query: 236 S-GLHYRWPDLPGP----QLETR-IEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGK 289 G +Y P LP P +LE R IE +L A AFARAN D L ++AR GIVT GK Sbjct: 245 GRGFNYD-PKLPWPSERTELERRIIEERLPAALAFARANPFDNTLVRPRDARVGIVTVGK 303 Query: 290 GHLDLLEALDLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGII 349 H D+L AL LG+D + +G+ +YKVGM WPLE G+ +F G ++V+EEKR + Sbjct: 304 AHGDVLSALAKLGLDAAEMERLGIGLYKVGMTWPLETAGVHNFARGMSALMVVEEKRSFV 363 Query: 350 ESQIKEYMSEPDRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLG-RFFEVDF- 407 E QIKE + + GK+ L+P ELSP VA L L VD Sbjct: 364 ERQIKESLFNVKASERPDVFGKELGDNSSLVPATLELSPGQVADSLRKFLAYTNVAVDVP 423 Query: 408 ------SERMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMAS 461 S +T +D + R P+FC+GCPHNTSTK+P+GS A AGIGCH MA Sbjct: 424 TPAPIASSGRKSFPILTDGED-SVLTRKPFFCAGCPHNTSTKLPDGSYAAAGIGCHIMAL 482 Query: 462 WMGRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITY 521 +T + QMGGEG+ W+G S +T PH+F NLG+GTY HSGS+AIRQAVAA N+TY Sbjct: 483 GDAGSTATFCQMGGEGIQWVGLSTFTEMPHMFINLGDGTYQHSGSLAIRQAVAAKANVTY 542 Query: 522 KILFNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTF 581 KILFNDAVAMTGGQP +G +TV R+ +Q+ AEGV V +++D+ KY P + Sbjct: 543 KILFNDAVAMTGGQPTEGGLTVRRVVEQVQAEGVASVTIVTDDTSKYAA---TAPGNAAV 599 Query: 582 HDRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGD 641 R ELD +QR+LR G +V++Y+QTCAAEKRRRRKR R IN VCEGCGD Sbjct: 600 VHRDELDSLQRDLRKKKGVSVIVYEQTCAAEKRRRRKRGTMRTAPARVVINPAVCEGCGD 659 Query: 642 CSVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGS 701 CSVQSNC+++ P TE+GRKR ++QS+CNKD SCV GFCPSFVT+EG + RK T + Sbjct: 660 CSVQSNCIAIEPLDTEVGRKRAVNQSTCNKDTSCVKGFCPSFVTVEGLEPRKPDQARTEA 719 Query: 702 V---LTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFM 758 V L ++L + P P PE+ ++V G+GGTGVVT+G +++MAAHLE RGAS LDF Sbjct: 720 VENELRQQLGN-PLPVPPEIRQHARIVVTGIGGTGVVTIGAILSMAAHLEGRGASTLDFT 778 Query: 759 GFAQKGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIV 818 G AQK G VLS+V++A S ++ RI A+ +I CD VVASS+ ALS L N T+ V Sbjct: 779 GLAQKNGAVLSHVQIASSRGEISTSRIERQSANVLIGCDAVVASSKDALSRLVFNSTQTV 838 Query: 819 ANEAELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMM 878 N PT+D+V D + + AVG+ + N AE + GD++ N+MM Sbjct: 839 INTHITPTSDFVKNGDLALSESAHRKSIVAAVGDATSIFWNCNAAAETIFGDSIACNMMM 898 Query: 879 LGFAWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVV 938 +GFA+Q+G++PLSEAA+M+AIELNG A+ NK AF WGRL A D A+ L + V Sbjct: 899 VGFAFQRGMIPLSEAAIMRAIELNGAAVSMNKRAFLWGRLIAHDGCAIDRLTETP----V 954 Query: 939 EVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQL 998 V+ + LD+ + +R L +YQN +A +Y+ V V E + LT + A+ Sbjct: 955 CVEEQFDLDQFVRSRMDDLTSYQNAAYAQRYKMLVDHVSAVERRVRGAVGDLTASAARSY 1014 Query: 999 YRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFG 1058 ++ +AYKDEYEVARL ++ F K + ETFEG+ K +H+APP++S GR K G Sbjct: 1015 FKVLAYKDEYEVARLHSDGSFSKRLAETFEGEGKFTYHMAPPVISRVDSRTGRRNKVALG 1074 Query: 1059 PWMFR-AFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETF 1117 W + R+L + LRG+ +DPF +DR+L+RA++++++ V+ L+ +N++ Sbjct: 1075 GWWLKPMLRVLKHGKLLRGSVLDPFSRQSDRRLERALIREFEDDVELALAHLSLTNHKAA 1134 Query: 1118 LQLAELPADVRGYGPVREQAAESIREKQTQLIKALDTG 1155 L L LP +RG+G V+E + ++ ++++ L G Sbjct: 1135 LDLITLPLAIRGFGVVKENSYKAAQQRRCAYRTELSNG 1172 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: 2965 Number of extensions: 128 Number of successful extensions: 7 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: 1172 Length of database: 1176 Length adjustment: 47 Effective length of query: 1125 Effective length of database: 1129 Effective search space: 1270125 Effective search space used: 1270125 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