Align Aldehyde:ferredoxin oxidoreductase,tungsten-containing; EC 1.2.7.- (characterized, see rationale)
to candidate WP_011385299.1 AMB_RS14710 aldehyde ferredoxin oxidoreductase
Query= uniprot:Q5P143 (616 letters) >NCBI__GCF_000009985.1:WP_011385299.1 Length = 616 Score = 864 bits (2233), Expect = 0.0 Identities = 414/617 (67%), Positives = 498/617 (80%), Gaps = 2/617 (0%) Query: 1 MGWNRKVLRVNLAEGTCTPEPLNMQWADEYLGSRGLATKYLVSETDPKVDPLSPDNKMIM 60 M W K LR++L G+ E LN WA +YLG RGLATKY E DPKVDPLSP NKMI Sbjct: 1 MSWTGKFLRIDLTNGSVKTEELNRAWARQYLGQRGLATKYFAEEVDPKVDPLSPANKMIF 60 Query: 61 ATGPLTGTMASTGGRYTVVTKGPLTGAIACSNSGGFFGAEMKFAGWDMVIFEGRSPTPVY 120 TGPLTGT ASTGGRY+VVTKGPLT IACSNSGGFFG E+K AGWDM+I EGRSP PVY Sbjct: 61 TTGPLTGTAASTGGRYSVVTKGPLTNCIACSNSGGFFGNELKNAGWDMIIVEGRSPKPVY 120 Query: 121 LFIENERAELRDASYLWGRSCWETEESIRAQHQDPLIRVSSIGRAGENQVMFACIVNDLH 180 L IENE E+RDA+ WG++ WETE ++A+HQDP++RV++IG AGE V++ACIVNDLH Sbjct: 121 LSIENETVEIRDAAEFWGKTVWETENGLKARHQDPMLRVATIGAAGEKGVLYACIVNDLH 180 Query: 181 RAAGRSGVGAVMGSKNLKAVAIRGTKGVSGIRDFPGFVRATSEAKKVLAGNPVTSEGLPK 240 RAAGRSGVGAVMGSKNLKA+A+RGT+GV+ ++D F++AT E KKVLA N VT +GLPK Sbjct: 181 RAAGRSGVGAVMGSKNLKAIAVRGTRGVT-VKDPDRFIKATIEQKKVLADNAVTGQGLPK 239 Query: 241 FGTQVLMNVINEMGALPTRNHRDVQFEDASKISAEAMHEKRPSDGKPQLVTNAACFGCTI 300 +GTQVLMNVINE+GA+PTRN ++VQFE A KISAEAMHE R +DGK L TN ACFGCTI Sbjct: 240 YGTQVLMNVINEIGAMPTRNFKEVQFEGAHKISAEAMHEPRATDGKANLATNGACFGCTI 299 Query: 301 ACGRISAIDKTHFTVKNNPKYWGASGGLEYEAAWALGAANGVGDLEALQYANLLCNEQGM 360 ACGRIS +D HF++ + P+Y SGG+EYEAAWA+G+ GV DLEA +AN +CNE G+ Sbjct: 300 ACGRISRMDPGHFSITSRPQYKEPSGGVEYEAAWAMGSDCGVDDLEACTFANFMCNEHGI 359 Query: 361 DPISFGATVGAAMELYETGVLTKERIG-LDAPFGSADALAKLAEMTATGEGFGKEIGLGS 419 DPISFG+T+ AAME++E GV+TKE+ G ++ FGSA+AL K+AE+T GEGFG E+G GS Sbjct: 360 DPISFGSTLAAAMEMFEMGVITKEQTGGVELKFGSAEALVKMAELTGKGEGFGLELGQGS 419 Query: 420 KRLCEKYGHPELSMSVKGQEFPAYDSRGIQGMGLAYATSNRGACHLRGYTVASEVLGVPV 479 +RLC KYGHPELSM+VK QEFPAYD RGIQGMGL YATSNRGACHLR YTVASEVLG+P Sbjct: 420 RRLCAKYGHPELSMTVKSQEFPAYDPRGIQGMGLTYATSNRGACHLRSYTVASEVLGIPF 479 Query: 480 KTDPHVIEGKAELVKAFQDATAVFDSAGICVFTSFAWTLADVQPQIAAACDGDWSMDKLA 539 K+DP +GKA LVKAFQDATA FD++GIC+FT+FAW+L ++ PQI AAC+G+W+ + L Sbjct: 480 KSDPLATDGKAALVKAFQDATAAFDASGICIFTTFAWSLENLAPQIDAACEGEWTPEILL 539 Query: 540 TVGERIWNMERQFNNAAGLGAQDDNLPPRLTSEPAKSGPAKGMVNRLAEMLPEYYGVRGW 599 VGERIW +ERQFN AAG+ A DD LP RL + AK+GPAKG+ + L +MLPEYY +RGW Sbjct: 540 EVGERIWTLERQFNLAAGMTAADDTLPKRLLKDAAKTGPAKGLTSGLEKMLPEYYQLRGW 599 Query: 600 TPEGTPTPETLSRLGLS 616 T +G PT ETL RL L+ Sbjct: 600 TTDGVPTTETLKRLQLA 616 Lambda K H 0.316 0.133 0.404 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: 1282 Number of extensions: 43 Number of successful extensions: 3 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: 616 Length of database: 616 Length adjustment: 37 Effective length of query: 579 Effective length of database: 579 Effective search space: 335241 Effective search space used: 335241 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 (21.6 bits) S2: 53 (25.0 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