Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_011841122.1 RSPH17029_RS08070 indolepyruvate ferredoxin oxidoreductase family protein
Query= reanno::psRCH2:GFF3452 (1156 letters) >NCBI__GCF_000015985.1:WP_011841122.1 Length = 1128 Score = 1053 bits (2724), Expect = 0.0 Identities = 571/1146 (49%), Positives = 764/1146 (66%), Gaps = 30/1146 (2%) Query: 1 MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60 MS +++L D+ L+ + L GTQA+ RL ++Q RD+A G NT G+++GYRGSPLG + Sbjct: 1 MSRQDVKLSDRTDLSKSPVLLNGTQAMVRLMLMQKARDRAEGRNTAGYVTGYRGSPLGAV 60 Query: 61 DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120 D ++ A LK I FQPG+NE+LAATAVWGSQQ L ++DGVFA+WYGKGPGVD Sbjct: 61 DLTMARAEKDLKAADILFQPGLNEDLAATAVWGSQQAELRGEGRFDGVFALWYGKGPGVD 120 Query: 121 RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180 R GDV +HAN AG SP GGVL+ GDDH +SST HQS+ A + A IPVL+PA VQEIL Sbjct: 121 RTGDVMRHANMAGTSPWGGVLMAMGDDHTGESSTTLHQSDWAMVDAYIPVLSPAGVQEIL 180 Query: 181 DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240 DYG+ GW LSR++G WV LKT+ + V+++AVV+ P R+Q PE F +PE G++IR D Sbjct: 181 DYGLYGWALSRFAGVWVGLKTMKDTVEATAVVDGRPDRMQFVRPE-FRMPEGGLNIRLVD 239 Query: 241 PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300 P+AQE R+ +K +AA AF+ AN ++R + P ++G ++ GKS+LD+ AL LG+ Sbjct: 240 TPVAQEARMIDHKRFAAEAFSHANGMDRRVWGRPGAKIGFVSAGKSWLDLVHALSLLGVG 299 Query: 301 EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360 EA +G+ KVG WP++ ++A+GLD I+ VEEKR +IE Q ++N + Sbjct: 300 EAEAERLGITTYKVGQVWPMDFRGFRDWAEGLDLIVCVEEKRKLIEVQAKEAIFN--DRR 357 Query: 361 RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPI-YTSDSIQARLAFLAAKEKALA 419 R+ G +++G L P L P IA I K L +D ++A LA LA +A Sbjct: 358 GRRIYGWQNDRGEELFPTRYALDPIGIAEKIGKILIEEGRGTDRVKAGLAQLAEARRADN 417 Query: 420 ARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNW 479 A+ + R P++CSGCPHNSST++PEGSRA AGIGCHYMVQWMDR T FTQMGGEG NW Sbjct: 418 AQDLA-ARLPYFCSGCPHNSSTRLPEGSRAYAGIGCHYMVQWMDRDTVGFTQMGGEGANW 476 Query: 480 IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539 IG+APF+ PH+FQNLGDGTY HSG A+RAA+AAG +TYKIL+NDAVAMTGGQ +G Sbjct: 477 IGEAPFSKRPHVFQNLGDGTYNHSGVQAIRAALAAGTTITYKILFNDAVAMTGGQTNEGG 536 Query: 540 LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599 L D++ R+I GVKRIA+V D ++ F H R E+ AVQR+ +GVS Sbjct: 537 LSADRIVREIQAMGVKRIAVVHDAKEEV-DLSRFPSGIEIHERAEMMAVQRDFATVEGVS 595 Query: 600 VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659 I+Y QTCA EKRRRRKRG D KR FIN VCEGCGDCG +SNC++++P+ETELGRK Sbjct: 596 AIVYIQTCAAEKRRRRKRGTFPDIDKRVFINTEVCEGCGDCGVQSNCVSIVPVETELGRK 655 Query: 660 REIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVL 719 R IDQ++CNKDFSC+EGFCPSFVT+ G +K A IE LPEP P + +N+L Sbjct: 656 RAIDQSSCNKDFSCLEGFCPSFVTLEGAKPKK--AATAEIELPDLPEPDLPAIRGSYNLL 713 Query: 720 IPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRI 779 + GVGG+GV T+GA+L MAAHL+G+G +++ AGLAQK G V H RIA K SDI A+R+ Sbjct: 714 VTGVGGTGVVTVGAILSMAAHLDGRGAAMMEMAGLAQKGGAVQIHCRIAEKPSDISAIRV 773 Query: 780 AAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQA 839 A GEAD ++G DL+V AG ++L +++ + AVVNSH+ T EFTRN D +VP ++ + Sbjct: 774 AVGEADGVIGGDLVVTAGAKTLGLMSQGRTGAVVNSHDIVTGEFTRNTDFRVPSDRLQVS 833 Query: 840 ISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVS 899 + + D+ F+DAT LA L+GDSI +N+ + G A+Q+GL+P+SAEAI++AIELNG + Sbjct: 834 LQARL-QDRVAFLDATELARILMGDSIYSNMMVFGAAWQRGLIPLSAEAIQRAIELNGAA 892 Query: 900 AKLNLQAFRWGRRAVLEREAVEQ--LARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLA 957 N +AF GR AVL ++ L P V+P+ +R + L YQS LA Sbjct: 893 VAQNARAFTLGRWAVLHPAEADRILLPEPPAPVDPVA--------YRAERLVGYQSRRLA 944 Query: 958 RRYRQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEG 1017 RR+R LV DSA + + VAR Y++LLAYKDEYEVARL+ + ++ +A+F+G Sbjct: 945 RRFRTLV------DSAPP-EIREDVARGYYQLLAYKDEYEVARLHLDT--LERAKAEFDG 995 Query: 1018 DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRR 1077 D++ FHLAP +LA + P+KR G W+L F +LA + LRGT LDPF +R+ Sbjct: 996 DFRPTFHLAPPFLAGKG--EERPKKRAFGRWMLPAFRLLAALKPLRGTALDPFARNPERQ 1053 Query: 1078 VERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLR 1137 +ER+LI+E+E + E L QL+P +A LP IRGYGPVKE + A + + L Sbjct: 1054 LERRLIAEFEDDMAEFLPQLRPETMELGRELARLPLSIRGYGPVKEANATTAALRREALL 1113 Query: 1138 EQLAKG 1143 + G Sbjct: 1114 AAIRAG 1119 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: 2856 Number of extensions: 120 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: 1156 Length of database: 1128 Length adjustment: 46 Effective length of query: 1110 Effective length of database: 1082 Effective search space: 1201020 Effective search space used: 1201020 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 (21.8 bits) S2: 58 (26.9 bits)
This GapMind analysis is from Apr 10 2024. 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