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_076948421.1 C1M55_RS23815 indolepyruvate ferredoxin oxidoreductase family protein
Query= reanno::psRCH2:GFF3452 (1156 letters) >NCBI__GCF_002893965.1:WP_076948421.1 Length = 1151 Score = 825 bits (2132), Expect = 0.0 Identities = 488/1140 (42%), Positives = 664/1140 (58%), Gaps = 47/1140 (4%) Query: 8 LDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWEA 67 LDD+ R +G + LTG QA+ R + QH RD G F+SGY+GSPLGG+DK L Sbjct: 16 LDDRCRSGSGPVLLTGVQAIARGFVEQHVRDIRAGKRIATFVSGYQGSPLGGVDKMLHGM 75 Query: 68 RDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPG-AKYDGVFAMWYGKGPGVDRAGDVF 126 L +H I F PG NEELAATAVWGSQ T+L G A +DGV +WYGKGPGVDRA D Sbjct: 76 PKVLAEHDITFIPGFNEELAATAVWGSQ-TDLPAGTATHDGVTGVWYGKGPGVDRATDTI 134 Query: 127 KHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIG 186 +HAN GV+P+GGV+LL GDD KSST+P SE + A +PVL P N +EI+ G+ Sbjct: 135 RHANMYGVNPKGGVVLLVGDDPASKSSTVPAVSERSLAAMGVPVLFPRNAEEIITMGMHA 194 Query: 187 WELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPE-DFE-LPEDGVHIRWPDPPLA 244 LSR SGC VALK +A+ D + ++ +PE FE P + PP + Sbjct: 195 VALSRVSGCVVALKIVADVADGAWTIDGSIADFDIVVPEVQFEGKPFVYKQRQMAAPPDS 254 Query: 245 QEKRLNLY--KIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEA 302 +LY + A+ ANNL+ + ++ ++GI TG ++ VRQAL DLG+D+A Sbjct: 255 VIAEADLYGPRWDLVHAYGTANNLDVIEVNPSGAKIGIAATGTTFDSVRQALADLGVDDA 314 Query: 303 LCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRP 362 G+R+L++GM +P+ + EFA+GL++I+VVE+K + IE Q+ LY P Sbjct: 315 ALHRAGIRLLRIGMCYPVVGEKIKEFAEGLEQIVVVEDKTAFIEAQIREVLYG--TDDAP 372 Query: 363 RVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARS 422 R++G+ D QG L+P ELT + + + L P + L+ Sbjct: 373 RIIGKRDGQGRLLMPASGELTAGRLLAPLRRVLKP---------HVELKRTLPAPLSLNV 423 Query: 423 YSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTET---FTQMGGEGVNW 479 S RT ++CSGCPHN ST +PEGS GIGCH +V R TQMGGEG W Sbjct: 424 LSAKRTAYFCSGCPHNRSTAIPEGSIGGGGIGCHTLVTMSGREDSAVTGLTQMGGEGSQW 483 Query: 480 IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539 IGQAPFTD PH+FQN+GDGT+FHSG LAV+A +AAGVN+TYK+LYN+ VAMTG Q +G Sbjct: 484 IGQAPFTDVPHLFQNIGDGTFFHSGQLAVQACIAAGVNITYKLLYNEVVAMTGAQDAEGA 543 Query: 540 LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599 L V QLS ++ EGVK+I + +DEP ++ R A T HR LD Q+ELRE KGV+ Sbjct: 544 LSVAQLSHKLTTEGVKQIIICADEPSRHNKR-ALAKGTKLWHRDRLDEAQKELREIKGVT 602 Query: 600 VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659 V+IYDQ CA + RR+RKRG + R IN AVCEGCGDCG KSNCL+V P++TE GRK Sbjct: 603 VLIYDQHCAADARRQRKRGTLPTRNTRVVINEAVCEGCGDCGVKSNCLSVQPVDTEYGRK 662 Query: 660 REIDQNACNKDFSCVEGFCPSFVTVH-GGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNV 718 +IDQ +CN D++C++G CPSFVTV G + P+A + +P L NV Sbjct: 663 TKIDQTSCNTDYTCMDGDCPSFVTVELVPGKKAPKAARP--VPPVVADPDFGPLTSTQNV 720 Query: 719 LIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVR 778 + G+GG+G+ T+ +L AA G LDQ GL+QK GPV +H+R ++ + + R Sbjct: 721 FLAGIGGTGIVTVNQVLATAALRAGLEVESLDQIGLSQKAGPVVSHLRFSSSALE-PSNR 779 Query: 779 IAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQ 838 + G AD ++ DL+ A +++L N + + ++ ++ ++ T + + + P Sbjct: 780 LTPGSADCIVAFDLLTATDNKNLDYGNAEKTVSIASTSQTPTGDMVYDKAVRYPEETSLL 839 Query: 839 AISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGV 898 A D V F DA A L G++ A N L+G AYQ G L + AEAIE+AI +NGV Sbjct: 840 ARLDKVSRTLRSF-DALAAAQELFGNTAAANFLLIGAAYQSGGLRLPAEAIEEAIGINGV 898 Query: 899 SAKLNLQAFRWGRRAVLEREAVEQLARPVDMV-EPIC-------------KTLEEIVDWR 944 + N+ AFRWGR A+ + A + P V EP+ +TL +V+ R Sbjct: 899 AVDANIAAFRWGRAAIADTAAFSAVTTPAKSVREPVVAPAHMFAGTTFTGETL-RLVELR 957 Query: 945 VDFLTRYQSAGLARRYRQLVERVRDADSA--DDLALSKAVARYYFKLLAYKDEYEVARLY 1002 L +QS +A+RY V+ V A+ A + S+AVAR FK AYKDEYEVAR+ Sbjct: 958 AAQLIEFQSVKIAQRYIDQVQAVWTAERAATERTDFSEAVARGLFKFTAYKDEYEVARML 1017 Query: 1003 SEPEFRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFL 1062 +P F + +++Q L + L P L V G +K LGP VLAK + L Sbjct: 1018 VDPAFIEDVKSQVPAGENLTYKLHPPILR----VMGRKKKIGLGPKSHVALKVLAKGKKL 1073 Query: 1063 RGTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVK 1122 RGT LDPFGY H R+VER+L++EYE + +L L Y AV IAALP+ +RGY +K Sbjct: 1074 RGTKLDPFGYMHVRKVERELLAEYEAMIADLSRTLATDGYDRAVEIAALPDVVRGYEDIK 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: 2853 Number of extensions: 136 Number of successful extensions: 11 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: 1151 Length adjustment: 47 Effective length of query: 1109 Effective length of database: 1104 Effective search space: 1224336 Effective search space used: 1224336 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 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