Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate HSERO_RS21380 HSERO_RS21380 MFS transporter
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__HerbieS:HSERO_RS21380 Length = 1199 Score = 1486 bits (3848), Expect = 0.0 Identities = 753/1195 (63%), Positives = 898/1195 (75%), Gaps = 26/1195 (2%) Query: 1 MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60 MNAPL P R L +VSL+DKYTLERGRV+++G QALVRLPMLQR+ D+ AGLNTA Sbjct: 1 MNAPL--PAGQ--RLLLDDVSLDDKYTLERGRVFMTGIQALVRLPMLQRQYDQRAGLNTA 56 Query: 61 GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120 GFI+GYRGSPLGA+DQ+ KA+++L A I F G+NEDLAATSVWG+QQVN++ A+++ Sbjct: 57 GFITGYRGSPLGAVDQTAEKARKYLEAKQIKFHPGMNEDLAATSVWGTQQVNLFKGAQYD 116 Query: 121 GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180 GVF +WYGKGPGVDR DVFKHAN AG+SRHGGVLV+AGDDHAAKSST AHQSEHI KAC Sbjct: 117 GVFSLWYGKGPGVDRCGDVFKHANMAGTSRHGGVLVIAGDDHAAKSSTAAHQSEHILKAC 176 Query: 181 GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240 G+PVLYPS+VQEYLDYGLH WAMSRY+GLWV+MKCVTD+VES SV +DP RV+I LP D Sbjct: 177 GIPVLYPSSVQEYLDYGLHGWAMSRYTGLWVAMKCVTDLVESGMSVMIDPERVQIQLPAD 236 Query: 241 FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300 F LPP GLNIR PD L QEAR+++YKWYA LAY RANK++RI DSP AR GI+T GK+ Sbjct: 237 FELPPDGLNIRQPDTVLGQEARMINYKWYAALAYARANKLNRIIWDSPRARIGIITAGKS 296 Query: 301 YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360 YLDTRQAL +LG+D++ IGIRLYKVG WPLEA G R FA+GL EILVVEEKRQI+E Sbjct: 297 YLDTRQALEDLGIDEQAARDIGIRLYKVGMTWPLEAEGVREFAQGLDEILVVEEKRQILE 356 Query: 361 YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQ----SNWLLPAHYELSPAIIARAI 416 Y LKEELYNWRDDVRP+V GKFD+ GEWS Q NWLLPA YEL+PA IARAI Sbjct: 357 YQLKEELYNWRDDVRPRVVGKFDDT----GEWSGSQREGHGNWLLPATYELNPAQIARAI 412 Query: 417 ATRLDKFELPADVRARIAARIAVIEAKEKAMAV---PRVAAERKPWFCSGCPHNTSTNVP 473 ATR+ ++ V ++ AR+A +EAKE + + P +R P FCSGCPHNTST +P Sbjct: 413 ATRISRYFAGHPVEQQVRARVAYLEAKEATLNISSKPDPDKDRIPHFCSGCPHNTSTKLP 472 Query: 474 EGSRALAGIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSG 533 EGSR LAGIGCHYM WMDR T F+ MGGEGV W+GQAPF +KHVFANLGDGTYFHSG Sbjct: 473 EGSRGLAGIGCHYMVTWMDRETKLFTHMGGEGVTWVGQAPFTDEKHVFANLGDGTYFHSG 532 Query: 534 LLAIRASIAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEP 593 LLA+RAS+AA VNITYKILYNDAVAMTGGQ DG L ++ Q+AAE R I+VVTDEP Sbjct: 533 LLAVRASVAAKVNITYKILYNDAVAMTGGQEFDGPLDPAMISRQLAAENVRPIIVVTDEP 592 Query: 594 EKYSAAIKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPA 653 +KY + +GV + HR ELD +QRELRE PG + +IYDQTCA+EKRRRRKR YPDPA Sbjct: 593 DKYPVGTQWAEGVTIRHRSELDAVQRELREQPGVSAMIYDQTCASEKRRRRKRNAYPDPA 652 Query: 654 KRAFINDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTA 713 KRA IN+AVCEGCGDCSV+SNCLSVEPLETE G KRQINQSSCNKD+SCVNGFCPSFVT Sbjct: 653 KRAVINEAVCEGCGDCSVQSNCLSVEPLETEFGRKRQINQSSCNKDYSCVNGFCPSFVTV 712 Query: 714 EGAQVKKPERHGVSM-DNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLE 772 EG Q+KKP R + LP+LP+P LPGL PYG+LVTGVGGTGV+TIG ++ MAAH+E Sbjct: 713 EGGQLKKPARAQADVGPALPSLPEPVLPGLAQPYGILVTGVGGTGVITIGQIIAMAAHVE 772 Query: 773 NKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVIS 832 + +VLDM+GLAQKGG V+SHV++A +H+TR+ G ADLVIGCD IV+A D +S Sbjct: 773 GRACSVLDMSGLAQKGGPVMSHVRVAEDAAHIHSTRVGTGMADLVIGCDVIVTASRDALS 832 Query: 833 KTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALI 891 + GRT A VN+ Q PTA F++NP WQFP S+E ++ A G + ++A +A AL+ Sbjct: 833 RMGEGRTHAAVNSTQMPTAAFVRNPDWQFPTASSEGEIARACGRDNLSLVDAGRIATALM 892 Query: 892 GDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLS 951 GDAI TN +LGYAWQKGW+PLS AL+RAIELN VE NK AF WGR AHD VL+ Sbjct: 893 GDAIATNMFMLGYAWQKGWVPLSEAALLRAIELNALQVEFNKQAFAWGRAAAHDVAFVLA 952 Query: 952 LTGKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAES 1011 G+ +A+ E + PT L++L+ R LT Y +AAYA+++RD V +VRA ES Sbjct: 953 AAGRNGMSAQVIEFKRTPT-----LDELVERRVAFLTDYLNAAYARSYRDFVEQVRARES 1007 Query: 1012 ALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNF 1071 AL G+ L L+ A A L KLMAYKDEYEVARL+ DP F K+ FEG DY+L F Sbjct: 1008 ALGEAGRGLKLSRAVASYLFKLMAYKDEYEVARLHADPAFRAKIAGMFEG----DYKLRF 1063 Query: 1072 WLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIG 1131 LAPPL+AKRD+KGHL K+ FG M +FGVLA+L+ LRG D F T ERR ERALI Sbjct: 1064 HLAPPLLAKRDDKGHLRKQAFGSWMMPVFGVLARLRFLRGTALDPFAYTEERRQERALIT 1123 Query: 1132 EYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQ 1186 EYRA L L L+ N +A +P++IRG+GHVK+ +L + ALL Q Sbjct: 1124 EYRATLSRLLDRLTPENLEQITAVARIPEEIRGYGHVKERHLKAAMEKQAALLAQ 1178 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: 3469 Number of extensions: 130 Number of successful extensions: 6 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 Apr 09 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