Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate NP_348620.1 CA_C2001 indolepyruvate ferredoxin oxidoreductase subunit alpha
Query= BRENDA::Q6LZB6 (578 letters) >NCBI__GCF_000008765.1:NP_348620.1 Length = 584 Score = 698 bits (1802), Expect = 0.0 Identities = 341/576 (59%), Positives = 437/576 (75%), Gaps = 1/576 (0%) Query: 1 MKKLMLGNEAVARGAYEAGVLVATAYPGTPSTEITEHISKYPEINSEWSVNEKVALEVAI 60 MKKLMLGNEA+ARGAYEAGV VATAYPGTPSTEITE I+KY E+ +EWS NEKVALEVAI Sbjct: 1 MKKLMLGNEAIARGAYEAGVTVATAYPGTPSTEITESIAKYHEVYAEWSPNEKVALEVAI 60 Query: 61 GSAIAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLIIVADDPSMHSSQNEQDTRYYG 120 GS+I GAR + SMKHVGLNVAADPL TV+YTGIN GL+I+VADDP MHSSQNEQD+R Y Sbjct: 61 GSSIGGARALCSMKHVGLNVAADPLFTVSYTGINGGLVIVVADDPGMHSSQNEQDSRRYA 120 Query: 121 IFSKIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLVELEEKEKIELK 180 +KIP+LEPS SQECK+FVK EISE+FD PVI+RLSTR++HSQ +VE+ E+ K ++K Sbjct: 121 KAAKIPMLEPSSSQECKEFVKEAYEISERFDCPVIIRLSTRIAHSQDIVEINERCKCDIK 180 Query: 181 PYDYNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNKIEYANKKIGIITSGVAYNY 240 Y + +KYV PA AK R I +E R+ +L +F++SS +N IE+ + IGII+SG+AY Y Sbjct: 181 DYIKDINKYVMVPAIAKVRHIKVESRMNKLVSFSESSQLNNIEWGKRNIGIISSGIAYQY 240 Query: 241 AKEAVSDASFLKFGMSYPLPEEKIKEFVQNCDKVYVFEELEPIFEQKIRSMGLNVIGKEI 300 A+E D S+LK GM YPLP E I+ F +++YV EELEP E+ I+ +G+ VIGKE+ Sbjct: 241 AREVFKDVSYLKIGMVYPLPREIIERFANKVEELYVIEELEPFIEEYIKELGIKVIGKEV 300 Query: 301 FPIVGELSSEIIRNALLNESKIVIEKI-EDLPQRPPVLCPGCHHRGPFYVLKKLKLHVAG 359 P+VGEL+SEII N+ ++ V +KI +D+ RPP +CPGC HRG FYVLKKLKL+V+G Sbjct: 301 LPMVGELNSEIINNSFSSKKPTVNKKIAKDIIARPPAMCPGCPHRGIFYVLKKLKLNVSG 360 Query: 360 DIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGKEFAKKSVAVIGDSTFWHSGVTG 419 DIGCY+LG PL +ID+ ICMGASIG+AHG E ARG EF ++VA++GDSTF HSG+TG Sbjct: 361 DIGCYSLGALLPLRSIDSCICMGASIGIAHGMEKARGTEFINRTVAILGDSTFIHSGITG 420 Query: 420 LIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTNQIDFEALGRSIGINRICV 479 LIDIVYNKG+STVIILDN++TAMTG+Q NP+TG + E T +++ E L R++G+ RI V Sbjct: 421 LIDIVYNKGNSTVIILDNAVTAMTGYQSNPTTGYNIKNEATKKVELEKLCRAVGVERIKV 480 Query: 480 VDAYDLKALEETIKEEVNAEEPSLIITKRPCVLIKGAKFDFKDYKIDPKLCTGCKLCLKA 539 VD +++ +E +KEE+ A EPS+II +R C IK K K++ C C+ CL+ Sbjct: 481 VDPFNVDEVESVVKEEIAACEPSVIIARRECERIKEHKSKAIPLKVNQSKCVKCRKCLEI 540 Query: 540 GCPAISFDGKVAKINDSLCVGCGLCKDLCKFSAIVE 575 GCP I + + +N SLC+GC LC ++CK A E Sbjct: 541 GCPCICIEDEDIVVNKSLCIGCKLCMNICKMDAFEE 576 Lambda K H 0.317 0.136 0.392 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: 1088 Number of extensions: 53 Number of successful extensions: 4 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: 578 Length of database: 584 Length adjustment: 36 Effective length of query: 542 Effective length of database: 548 Effective search space: 297016 Effective search space used: 297016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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