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_011766137.1 AZO_RS12140 MFS transporter
Query= reanno::psRCH2:GFF3452 (1156 letters) >NCBI__GCF_000061505.1:WP_011766137.1 Length = 1194 Score = 1107 bits (2864), Expect = 0.0 Identities = 589/1154 (51%), Positives = 764/1154 (66%), Gaps = 22/1154 (1%) Query: 5 EIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSL 64 + RL D + +G ++LTGTQAL RLP++Q D A G NTGGFISGYRGSPLG D+ L Sbjct: 13 DYRLADSLQAMSGQIFLTGTQALVRLPLMQAALDAAAGRNTGGFISGYRGSPLGAYDQQL 72 Query: 65 WEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGD 124 W+A+ L + I F P VNEEL ATAV G+QQ DGVFA+WYGKGPGVDRAGD Sbjct: 73 WKAKALLDANRIRFLPAVNEELGATAVLGTQQVEGDAERTVDGVFAIWYGKGPGVDRAGD 132 Query: 125 VFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGI 184 +H NA G SP GGVL + GDDHGC SS++PHQS+ A +PVLNPA+V E+L++G+ Sbjct: 133 ALRHGNAYGASPHGGVLAVIGDDHGCVSSSMPHQSDFTLQAWGLPVLNPASVAEMLEFGL 192 Query: 185 IGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD-PPL 243 GW LSRYSGCWV LK I+E V+S++ V++D +R + +F P G+H RWPD P L Sbjct: 193 YGWALSRYSGCWVGLKAISETVESASTVDLDAIRTRFDGVPEFTPPATGLHYRWPDLPSL 252 Query: 244 AQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEAL 303 E+RL+ K+ AARAFA AN +++ + +P +GI++ GK++LD+ +A LG+ A Sbjct: 253 VIEQRLHA-KLDAARAFAAANPIDKTICAAPQADIGIVSCGKAHLDLLEAFRRLGVSLAD 311 Query: 304 CASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPR 363 + G+R KVG S+PLE + FA GL EILVVEEK +IE Q+ YN ++RP Sbjct: 312 LEAAGIRFYKVGQSFPLETARMRAFATGLKEILVVEEKGPVIERQIKELFYNADPAERPL 371 Query: 364 VVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLA---AKEKALAA 420 V+G+ G LL L EL P+ + VIA LA +A + L+ Sbjct: 372 VIGKSGRDGAPLLSALGELRPSRVIPVIAAWLAGHRPEIEQRAHVVEHVTDFTPPPLLSN 431 Query: 421 RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWM-DRRTETFTQMGGEGVNW 479 + R P++CSGCPHN+STKVPEGS A AGIGCH+M WM DR T QMGGEGV+W Sbjct: 432 EADGVRRVPYFCSGCPHNTSTKVPEGSHAQAGIGCHFMASWMPDRETTGLIQMGGEGVDW 491 Query: 480 IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539 + + FT TPH+FQNLGDGTYFHSG LA+R A+AAG NVTYKILYNDAVAMTGGQP+DG Sbjct: 492 VAHSAFTRTPHVFQNLGDGTYFHSGFLAIRQAIAAGTNVTYKILYNDAVAMTGGQPVDGT 551 Query: 540 LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPI-TSFHHRRELDAVQRELREFKGV 598 + VD ++RQ+ EG +R+A+VSDEP+KY + P TSFHHR ELDAVQRELRE KGV Sbjct: 552 VTVDAIARQVEAEGARRVAVVSDEPEKYDGHEGLFPRGTSFHHRAELDAVQRELREVKGV 611 Query: 599 SVIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGR 658 +V+IYDQTCA EKRRRRK+ DPA+R FIN AVCEGCGDCG++SNCL+++P++T GR Sbjct: 612 TVLIYDQTCAAEKRRRRKKQAYPDPARRIFINDAVCEGCGDCGKQSNCLSIVPVDTPFGR 671 Query: 659 KREIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAA-------TLPEPQHPT 711 KR IDQ++CNKD+SCV GFCPSFV+V GG L+KP A +AA TLP P+ Sbjct: 672 KRAIDQSSCNKDYSCVNGFCPSFVSVLGGSLKKPTGPA--FDAARLDELVGTLPLPKAWC 729 Query: 712 LDRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQ 771 D P+++L+ GVGG+GV T+GAL+ MAAHLEGK +VLD G AQK G V + VR+ A Sbjct: 730 WDAPYDLLVTGVGGTGVVTVGALITMAAHLEGKSASVLDFMGFAQKGGQVLSFVRLGADA 789 Query: 772 SDIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQV 831 S + VRI A +AD +L CDL+V A +++L + V N HE TA F ++PDA + Sbjct: 790 SVLNQVRIDAQQADAILACDLVVGASNDALLTARHGRTRIVANVHEIQTARFVQDPDADL 849 Query: 832 PGAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEK 891 A+ + A G D+ DA L R LGD++ N+ L+G+A+Q+GL+P+S A+++ Sbjct: 850 HVDALLAKMRYAAGDDRLDTCDAQALCARFLGDTMGANILLMGYAWQRGLIPVSLAALDR 909 Query: 892 AIELNGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRY 951 AIELNGV+ +N AFR GR A EA+ LA + +L IV LT Y Sbjct: 910 AIELNGVAVAMNRSAFRIGRLAAAGAEALAALAAGPLAQPEVADSLGAIVALHAAHLTGY 969 Query: 952 QSAGLARRYRQLVERV----RDADSAD-DLALSKAVARYYFKLLAYKDEYEVARLYSEPE 1006 Q+A A RY +++V R A AD L L+ VAR Y KLLAYKDEYEVARLY++ Sbjct: 970 QNAAYAARYTAFIDKVAAAERKALGADAPLRLAPVVARTYGKLLAYKDEYEVARLYTDGR 1029 Query: 1007 FRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTP 1066 FRQ LEAQFEGDY+LQFH+AP LAK P G P+K + GP ++ L +LA R LRGT Sbjct: 1030 FRQALEAQFEGDYRLQFHMAPPLLAKPGP-NGRPKKMDFGPRLMPLLRLLAAARGLRGTA 1088 Query: 1067 LDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSI 1126 D FG +RR+ER+L ++Y + +D LL +L AV A L E +RG+GPVK ++ Sbjct: 1089 FDLFGRSEERRMERELAADYARAIDALLPRLAADTVDAAVEFAGLAEGVRGFGPVKLANL 1148 Query: 1127 AKARQQEKLLREQL 1140 +Q+E++L L Sbjct: 1149 RTVKQRERVLLHTL 1162 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: 3100 Number of extensions: 110 Number of successful extensions: 8 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: 1194 Length adjustment: 47 Effective length of query: 1109 Effective length of database: 1147 Effective search space: 1272023 Effective search space used: 1272023 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