Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_076948421.1 C1M55_RS23815 indolepyruvate ferredoxin oxidoreductase family protein
Query= reanno::Marino:GFF880 (1172 letters) >NCBI__GCF_002893965.1:WP_076948421.1 Length = 1151 Score = 708 bits (1827), Expect = 0.0 Identities = 430/1158 (37%), Positives = 634/1158 (54%), Gaps = 64/1158 (5%) Query: 7 QLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVD 66 Q Y L+DR SG V LTG QA+ R + Q D + G A VSGY+GSPLG VD Sbjct: 10 QAKPYDLDDRCRSGSGPVLLTGVQAIARGFVEQHVRDIRAGKRIATFVSGYQGSPLGGVD 69 Query: 67 QALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDR 126 + L +L E+ I F+P NE+LAAT + G+Q +GV G+WYGKGPGVDR Sbjct: 70 KMLHGMPKVLAEHDITFIPGFNEELAATAVWGSQTDLPAGTATHDGVTGVWYGKGPGVDR 129 Query: 127 AGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLE 186 A D ++H YG +P GGV+++ GDD SS++P S+ + + +P + P N E + Sbjct: 130 ATDTIRHANMYGVNPKGGVVLLVGDDPASKSSTVPAVSERSLAAMGVPVLFPRNAEEIIT 189 Query: 187 FGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAP-DFVTPD-------------DFT 232 G+ ALSR SGC V K +++ + A +++ A D V P+ Sbjct: 190 MGMHAVALSRVSGCVVALKIVADVADGAWTIDGSIADFDIVVPEVQFEGKPFVYKQRQMA 249 Query: 233 APESGLHYRWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHL 292 AP + DL GP+ + V A+ AN +D + A+ GI TG Sbjct: 250 APPDSVIAE-ADLYGPRWDL--------VHAYGTANNLDVIEVNPSGAKIGIAATGTTFD 300 Query: 293 DLLEALDLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQ 352 + +AL LG+D+ G+ + ++GM +P+ I +F G E+++V+E+K IE+Q Sbjct: 301 SVRQALADLGVDDAALHRAGIRLLRIGMCYPVVGEKIKEFAEGLEQIVVVEDKTAFIEAQ 360 Query: 353 IKEYMSEPDRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFE--VDFSER 410 I+E + D ++ GK+D GR L+P GEL+ AG L A L R + V+ Sbjct: 361 IREVLYGTDDAPRII--GKRDGQGRLLMPASGELT----AGRLLAPLRRVLKPHVELKRT 414 Query: 411 MAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTES- 469 + ++ KR YFCSGCPHN ST +PEGS GIGCH + + GR + Sbjct: 415 LPAPLSLNVLS----AKRTAYFCSGCPHNRSTAIPEGSIGGGGIGCHTLVTMSGREDSAV 470 Query: 470 --LIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFND 527 L QMGGEG WIG++ +T PH+FQN+G+GT+FHSG +A++ +AAG+NITYK+L+N+ Sbjct: 471 TGLTQMGGEGSQWIGQAPFTDVPHLFQNIGDGTFFHSGQLAVQACIAAGVNITYKLLYNE 530 Query: 528 AVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSEL 587 VAMTG Q +G ++V +++ ++ EGV ++++ +DEP +++ K R L Sbjct: 531 VVAMTGAQDAEGALSVAQLSHKLTTEGVKQIIICADEPSRHNKR--ALAKGTKLWHRDRL 588 Query: 588 DQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSN 647 D+ Q+ELR+I G TVLIYDQ CAA+ RR+RKR P R IN VCEGCGDC V+SN Sbjct: 589 DEAQKELREIKGVTVLIYDQHCAADARRQRKRGTLPTRNTRVVINEAVCEGCGDCGVKSN 648 Query: 648 CLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKL 707 CLSV P TE GRK KIDQ+SCN D++C++G CPSFVT+E + + + + Sbjct: 649 CLSVQPVDTEYGRKTKIDQTSCNTDYTCMDGDCPSFVTVE--LVPGKKAPKAARPVPPVV 706 Query: 708 ADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTV 767 AD P +T + ++ + G+GGTG+VTV Q++ AA LD +G +QK G V Sbjct: 707 AD---PDFGPLTSTQNVFLAGIGGTGIVTVNQVLATAALRAGLEVESLDQIGLSQKAGPV 763 Query: 768 LSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTA 827 +S++R + S + R++ G AD ++A DL+ A+ K L T +A+ ++ PT Sbjct: 764 VSHLRFSSSALEPSN-RLTPGSADCIVAFDLLTATDNKNLDYGNAEKTVSIASTSQTPTG 822 Query: 828 DYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGL 887 D V + + L + V DA A++L G+T +N +++G A+Q G Sbjct: 823 DMVYDKAVRYPEETSLLARLDKVSRT-LRSFDALAAAQELFGNTAAANFLLIGAAYQSGG 881 Query: 888 LPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDP---SAVTDLLDDSNAQVV------ 938 L L A+ +AI +NGVA+D N AF WGR + D SAVT VV Sbjct: 882 LRLPAEAIEEAIGINGVAVDANIAAFRWGRAAIADTAAFSAVTTPAKSVREPVVAPAHMF 941 Query: 939 --EVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQ 996 TL L+ R L+ +Q+ + A +Y D V V AE + E + AVA+ Sbjct: 942 AGTTFTGETL-RLVELRAAQLIEFQSVKIAQRYIDQVQAVWTAERAATE-RTDFSEAVAR 999 Query: 997 QLYRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRR 1056 L++F AYKDEYEVAR+ + F+++V + + L PP+L GR KK Sbjct: 1000 GLFKFTAYKDEYEVARMLVDPAFIEDVKSQVPAGENLTYKLHPPILR----VMGRKKKIG 1055 Query: 1057 FGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYET 1116 GP A ++LAK + LRGT +DPF Y RK++R +L +Y++++ + R L Y+ Sbjct: 1056 LGPKSHVALKVLAKGKKLRGTKLDPFGYMHVRKVERELLAEYEAMIADLSRTLATDGYDR 1115 Query: 1117 FLQLAELPADVRGYGPVR 1134 +++A LP VRGY ++ Sbjct: 1116 AVEIAALPDVVRGYEDIK 1133 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: 2832 Number of extensions: 129 Number of successful extensions: 12 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: 1151 Length adjustment: 47 Effective length of query: 1125 Effective length of database: 1104 Effective search space: 1242000 Effective search space used: 1242000 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 24 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