Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_011767155.1 AZO_RS17245 MFS transporter
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >NCBI__GCF_000061505.1:WP_011767155.1 Length = 1198 Score = 1406 bits (3639), Expect = 0.0 Identities = 721/1191 (60%), Positives = 880/1191 (73%), Gaps = 41/1191 (3%) Query: 14 RRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGA 73 +R L N L+D+YTL GRVY+SG QALVRL M+Q ERD AAGL+TAGF+SGYRGSPLG Sbjct: 28 QRPLGN--LDDRYTLVSGRVYLSGYQALVRLLMIQSERDAAAGLHTAGFVSGYRGSPLGG 85 Query: 74 LDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGV 133 LDQ+LWKAKQHLAAHDIVFQ G+NEDLAAT+VWGSQQVN+ P AR++GVF MWYGKGPGV Sbjct: 86 LDQTLWKAKQHLAAHDIVFQPGVNEDLAATAVWGSQQVNLSPQARYDGVFAMWYGKGPGV 145 Query: 134 DRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEY 193 DR DVF+HAN+AGS+R GGVLV+AGDDHAAKSSTL HQ++H FK+ +PVL P+ VQEY Sbjct: 146 DRCGDVFRHANAAGSARFGGVLVIAGDDHAAKSSTLPHQTDHFFKSMMMPVLAPAGVQEY 205 Query: 194 LDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWP 253 +D+G+H +A+SRYSG WV+ K + D VE+SASV++DP RV++ P DF LPP GLNIRWP Sbjct: 206 IDFGVHGYALSRYSGCWVAFKALADTVETSASVDVDPQRVQVATPTDFPLPPDGLNIRWP 265 Query: 254 DPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGL 313 DPPL QE RLL +K YA LAY RAN+++R+ IDSP R GI+T GK+YLD RQA +LG+ Sbjct: 266 DPPLVQEKRLLHFKLYAALAYARANRLNRVVIDSPAPRLGIITSGKSYLDVRQAFDDLGI 325 Query: 314 DDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDD 373 DD A IGIRLYKVG VWPLE+ G R FAEGL EILVVEEKRQ++EY LKEELYNWR+D Sbjct: 326 DDALAAEIGIRLYKVGMVWPLESDGVRQFAEGLDEILVVEEKRQLLEYQLKEELYNWRED 385 Query: 374 VRPKVYGKFDEKDN----AGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADV 429 VRP+V GKFDEK A G+ +I +WLLPA EL+PA+IAR IA R+++F V Sbjct: 386 VRPRVIGKFDEKGEWARIARGDGTIDHGDWLLPAAGELNPALIARVIAGRIERF----FV 441 Query: 430 RARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTV 489 RI AR+A +EAK+ +A + +R P FCSGCPHN ST VPEGSRALAGIGCHYM Sbjct: 442 SERIRARLAFLEAKDHTLAQRVFSIDRVPTFCSGCPHNISTRVPEGSRALAGIGCHYMVT 501 Query: 490 WM-DRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNIT 548 WM DR T TF+QMGGEGV W+GQAPF ++H+FANLGDGTYFHSGLLAIR ++AAGVNIT Sbjct: 502 WMPDRRTGTFTQMGGEGVPWVGQAPFTHERHIFANLGDGTYFHSGLLAIRQAVAAGVNIT 561 Query: 549 YKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEV 608 YKIL+NDAVAMTGGQP++G L+V + Q+ AEG IVVVTD E+ A LP V + Sbjct: 562 YKILFNDAVAMTGGQPVEGGLTVPKIVRQLQAEGVHNIVVVTDGTERGYGAADLPH-VPI 620 Query: 609 HHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGD 668 HRDELD IQRELRE G T LIYDQTCA EKRRRRKRGT+PDPA+R FIN+AVCEGCGD Sbjct: 621 RHRDELDAIQRELRESGGVTALIYDQTCAAEKRRRRKRGTFPDPARRVFINEAVCEGCGD 680 Query: 669 CSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSM 728 C V+SNC+S+ P+ETE G KR I+QSSCNKD+SC+NGFCPSF+T EG + +K + Sbjct: 681 CGVQSNCMSILPVETEFGRKRAIDQSSCNKDYSCLNGFCPSFITVEGGRPRKGQALETDE 740 Query: 729 DNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKG 788 LP P LP E P+G+LVTGVGGTGVVTIG L+GMAAHL+ KGVTVLDM GLAQKG Sbjct: 741 SRFGELPPPRLPTTETPFGILVTGVGGTGVVTIGALIGMAAHLDGKGVTVLDMTGLAQKG 800 Query: 789 GAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQT 848 G+V SH++IA P+ LHA RIA GEAD VIG D IVSA + + K RTRA+VN A+T Sbjct: 801 GSVFSHIRIAERPEDLHAVRIAAGEADAVIGGDIIVSASVEALGKMSAERTRAVVNLAET 860 Query: 849 PTAEFIKNPKWQFPGLSAEQDVRNAVGEA-----CDFINASGLAVALIGDAIFTNPLVLG 903 PT++F +NP W+FP ++ A+GEA DFI+A +A L+GDAI TN +LG Sbjct: 861 PTSDFARNPDWRFP----LDQMKTAIGEATRPGGVDFIDAQSIATRLLGDAIATNLFLLG 916 Query: 904 YAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGA 963 YAWQKG +P+ L+AL++AI LNG A+ N+ AF WGR AHDP VL+L A A Sbjct: 917 YAWQKGLVPVRLEALMQAITLNGVALALNRKAFLWGRRAAHDPAAVLAL-------AHPA 969 Query: 964 EVVKL--PTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLP 1021 V+L PT L+++++ RA L+AYQDAAYA +R VS+VR E+ V Sbjct: 970 PPVRLHPPT-----LDEVVSIRANFLSAYQDAAYADRYRRLVSQVREQEARAVSPAS-TR 1023 Query: 1022 LTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKR 1081 L EA ARN KL+AYKDEYEVARLY DP F ++ FEG DY++ F LAPP +A+ Sbjct: 1024 LAEAVARNYFKLLAYKDEYEVARLYVDPAFWARVDETFEG----DYEVRFHLAPPFLARL 1079 Query: 1082 DEK-GHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEEL 1140 D + G + K+ FG + + +F LA+L+ +RG +D+FG TAERR ERALI +Y A + EL Sbjct: 1080 DPRTGRIPKKAFGAAVLHVFRWLARLRRVRGTRWDIFGYTAERRAERALITQYEADVAEL 1139 Query: 1141 TRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPE 1191 LS A A+ +A +PD IRGFG +K N+ + R ALL +R E Sbjct: 1140 LASLSEPRLALAVDIAGIPDVIRGFGPIKARNMEEAARRRAALLATWRDAE 1190 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: 3488 Number of extensions: 129 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: 1197 Length of database: 1198 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1151 Effective search space: 1323650 Effective search space used: 1323650 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 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