Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate BPHYT_RS18305 BPHYT_RS18305 MFS transporter
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__BFirm:BPHYT_RS18305 Length = 1199 Score = 1820 bits (4713), Expect = 0.0 Identities = 888/1201 (73%), Positives = 1021/1201 (85%), Gaps = 14/1201 (1%) Query: 1 MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60 MNAPL ++ AL++V+L+DKYTLERGR Y+SG QALVRLPMLQ+ERDRAAGLNTA Sbjct: 1 MNAPLDAGQRASLEAALSSVTLDDKYTLERGRAYMSGIQALVRLPMLQQERDRAAGLNTA 60 Query: 61 GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120 GFISGYRGSPLG LDQSLWKAKQHLAAH +VFQ G+NEDLAAT+VWGSQQVN+YP A+++ Sbjct: 61 GFISGYRGSPLGGLDQSLWKAKQHLAAHQVVFQPGVNEDLAATAVWGSQQVNLYPSAKYD 120 Query: 121 GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180 GVF MWYGKGPGVDR+SDVFKH NSAGS+R+GGVLVLAGDDHAAKSSTLAHQSEHIFKAC Sbjct: 121 GVFSMWYGKGPGVDRSSDVFKHGNSAGSARNGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180 Query: 181 GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240 GLPVL+PSNVQEYLD+GLH WAMSRYSGLWV+MKCVTDVVESSASV++DPHR +I+LP+D Sbjct: 181 GLPVLFPSNVQEYLDFGLHGWAMSRYSGLWVAMKCVTDVVESSASVDIDPHRTKIILPED 240 Query: 241 FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300 F +P GGLNIRWPDPPL QEARLLDYKWYA LAYVRANK+DR+EIDSPHARFGIMTGGKA Sbjct: 241 FAMPEGGLNIRWPDPPLVQEARLLDYKWYAALAYVRANKLDRVEIDSPHARFGIMTGGKA 300 Query: 301 YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360 YLD RQAL +LGLDDETC+RIGIRLYKVGCVWPLEA GA+AFA GL EILVVEEKRQI+E Sbjct: 301 YLDVRQALTDLGLDDETCSRIGIRLYKVGCVWPLEAQGAQAFARGLDEILVVEEKRQILE 360 Query: 361 YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420 YA+KEELYNW D RP+V+GKFDEKD AGGEWS+P NWLLPAHYELSPAIIA+AIATRL Sbjct: 361 YAIKEELYNWPDAQRPRVFGKFDEKDGAGGEWSVPMGNWLLPAHYELSPAIIAKAIATRL 420 Query: 421 DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480 DKF+LP+DVRARIA RIAVIEAKEKA+A PRV AERKPWFCSGCPHNTSTNVPEGSRA+A Sbjct: 421 DKFDLPSDVRARIATRIAVIEAKEKALARPRVEAERKPWFCSGCPHNTSTNVPEGSRAMA 480 Query: 481 GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540 GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPF+ DKHVFANLGDGTYFHSGLLAIRA+ Sbjct: 481 GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFSNDKHVFANLGDGTYFHSGLLAIRAA 540 Query: 541 IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAI 600 IA+ NITYKILYNDAVAMTGGQP+DG L+V + +Q+AAEGA KIV+VTDEPEKYSA + Sbjct: 541 IASKANITYKILYNDAVAMTGGQPVDGVLTVPQITHQLAAEGATKIVIVTDEPEKYSANV 600 Query: 601 KLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIND 660 L G+++HHRD+LD +QR+LREVPG TILIYDQTCATEKRRRRKRGTYPDPA+R IN+ Sbjct: 601 GLAPGIDIHHRDKLDEVQRQLREVPGTTILIYDQTCATEKRRRRKRGTYPDPARRVVINE 660 Query: 661 AVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKK 720 AVCEGCGDCSVKSNCLSVEPL+TE GTKRQINQS+CNKDFSCVNGFCPSFV+ EG Q++K Sbjct: 661 AVCEGCGDCSVKSNCLSVEPLDTEYGTKRQINQSTCNKDFSCVNGFCPSFVSVEGGQLRK 720 Query: 721 PE-RHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVL 779 P+ G++ D +P +P+P LP +E PYGVLVTGVGGTGVVTIG LLGMAAHLENKGVTVL Sbjct: 721 PKAASGLAGDAMPPVPEPDLPSMERPYGVLVTGVGGTGVVTIGALLGMAAHLENKGVTVL 780 Query: 780 DMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRT 839 D+ GLAQKGGAV+SHVQIA +P +HATRIAMGEA LVIGCDAIV+A D+ +S+ Q GRT Sbjct: 781 DVTGLAQKGGAVMSHVQIAKNPADIHATRIAMGEASLVIGCDAIVTASDECVSRMQAGRT 840 Query: 840 RAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFTN 898 R ++N+A TPTAE IKNP W+FPG S E DVR A G + D ++A+ AVAL+GDAI+TN Sbjct: 841 RVVLNSAHTPTAELIKNPNWRFPGSSTEADVRAAAGDDGVDTVDANHFAVALLGDAIYTN 900 Query: 899 PLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLT----- 953 P VLGYAWQ+GW+PL+ +L+RAIELN VEKN+AAF+WGR AHD V L Sbjct: 901 PFVLGYAWQRGWVPLTYQSLMRAIELNNVQVEKNRAAFEWGRRAAHDLAGVRKLAQSQGR 960 Query: 954 GKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESAL 1013 G TA ++++ L T L+ LI RAE+LTA+Q++AYA +R VS+VRAAESAL Sbjct: 961 GAAAETA-SSKIISLHTPKA--LDTLIDKRAEYLTAWQNSAYADRYRALVSQVRAAESAL 1017 Query: 1014 VGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWL 1073 LPLTEA A+NL KLMAYKDEYEVARLY+DP F++KL+ FEG D++L+ L Sbjct: 1018 DSIDGQLPLTEAVAKNLHKLMAYKDEYEVARLYSDPAFIEKLKANFEG----DWKLHIHL 1073 Query: 1074 APPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEY 1133 APP +K+D KGHLVK+++GP VLA+LK LRG DVFGKT ERRTERALIGEY Sbjct: 1074 APPTFSKKDAKGHLVKKKYGPWVFSAMHVLARLKFLRGTALDVFGKTEERRTERALIGEY 1133 Query: 1134 RALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETA 1193 AL+ EL GL+A A+ LA+LPD IRG+GHVK++NL VR +W LL ++R PE Sbjct: 1134 EALVRELIAGLTAQKRELAVELANLPDGIRGYGHVKENNLKGVRVKWNELLARWRSPEAG 1193 Query: 1194 Q 1194 + Sbjct: 1194 K 1194 Lambda K H 0.319 0.135 0.407 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: 3655 Number of extensions: 133 Number of successful extensions: 5 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: 1197 Length of database: 1199 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1152 Effective search space: 1324800 Effective search space used: 1324800 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: 59 (27.3 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