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 BPHYT_RS02015 BPHYT_RS02015 MFS transporter
Query= reanno::psRCH2:GFF3452 (1156 letters) >FitnessBrowser__BFirm:BPHYT_RS02015 Length = 1195 Score = 1089 bits (2816), Expect = 0.0 Identities = 577/1168 (49%), Positives = 773/1168 (66%), Gaps = 27/1168 (2%) Query: 2 SLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLD 61 +LA+ +L D G ++LTGTQAL RL ++Q D+ARG+NT GFISGYRGSPLG +D Sbjct: 12 ALADYKLSDNLTATRGRIFLTGTQALVRLVLMQRAADKARGMNTAGFISGYRGSPLGMVD 71 Query: 62 KSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDR 121 + LW+A+ L I F P +NEEL TAV G+Q+ P +GVFAMWYGKGPGVDR Sbjct: 72 QQLWKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFAMWYGKGPGVDR 131 Query: 122 AGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILD 181 AGD KH NA G SP GGVL++AGDDHGC SS++PHQS+ A +A +PV+NP+N+ ++L+ Sbjct: 132 AGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPVVNPSNIADMLE 191 Query: 182 YGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD- 240 +G+ GWELSR+SG WV K I+E V+S + V++D LR +P+DFE+P G+H RWPD Sbjct: 192 FGLYGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVPAGGLHNRWPDL 251 Query: 241 PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300 P L E R++ K+ A R FAR N++++ + SP+ +GI+T GK++LD+ + L L L Sbjct: 252 PSLTIESRMHA-KLDAVRHFARVNSIDKWIAPSPHANVGIVTCGKAHLDLMETLRRLDLT 310 Query: 301 EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360 A + G+R+ KVG+S+PLE + F GL E+LV+EEK +IE Q+ LYN Sbjct: 311 VADLEAAGVRIYKVGLSFPLEMTRIDAFVSGLSEVLVIEEKGPVIEQQIKDYLYNRTQGT 370 Query: 361 RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420 RP VVG+ E G LL +L EL P+ I V A LA + + R+ L A + L+ Sbjct: 371 RPIVVGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDLVAPQ-ILSN 429 Query: 421 RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI 480 + S RTP++CSGCPHN+STKVPEGS A AGIGCH+M WM+R T QMGGEGV+W Sbjct: 430 AADSVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQMGGEGVDWA 489 Query: 481 GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540 + FT T H+FQNLGDGTYFHSG LA+R AVAA +TYKILYNDAVAMTGGQP+DG + Sbjct: 490 SHSMFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMTGGQPVDGSI 549 Query: 541 RVDQLSRQIFHEGVKRIALVSDEPDKYPS-RDTFAPITSFHHRRELDAVQRELREFKGVS 599 V Q++RQ+ EGV R +VSDEP+KY D F T+FHHR E+D VQR+LR+ GV+ Sbjct: 550 SVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQRQLRDTDGVT 609 Query: 600 VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659 V+IYDQTCA EKRRRRK+G+ DP KR FIN VCEGCGDCG +SNCL+V P+ET LGRK Sbjct: 610 VLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVEPVETALGRK 669 Query: 660 REIDQNACNKDFSCVEGFCPSFVTVHGGGLRK-------PEAVAGGIEAATLPEPQHPTL 712 R IDQ++CNKD+SCV GFCPSFVTV GG L+K P+A+A +EA LP P Sbjct: 670 RRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAARVEA--LPIPATHLD 727 Query: 713 DRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQS 772 P+++L+ GVGG+GV T+GAL+ MAAHLEGK +VLD G AQK G V + VR AA+ Sbjct: 728 AAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDE 787 Query: 773 DIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVP 832 + VRI +AD+LL CD++V A ++L + + VVN+H A F NPDA + Sbjct: 788 WLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVTNPDATLH 847 Query: 833 GAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKA 892 A+ + A GA++ DA LATR LGD+I N+ +LG+A+Q GL+P+S A+ +A Sbjct: 848 ADALLDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGAMMRA 907 Query: 893 IELNGVSAKLNLQAFRWGRRAVLEREAVEQL--ARPVDMVEPICKTLEEIVDWRVDFLTR 950 IELN V+ ++N AF GR A + A+E L AR + TL+E++ R L Sbjct: 908 IELNNVAVQMNQLAFSIGRLAAEDPAALEALWQARHLAKQSVRVDTLDELIAHREGRLQT 967 Query: 951 YQSAGLARRYRQLVERVRDADSADDL---ALSKAVARYYFKLLAYKDEYEVARLYSEPEF 1007 Y A +RYR LV+ R A+++ D +++AVA +++LLA KDEYEVARL+++ F Sbjct: 968 YGGASYVKRYRALVDAARRAETSVDAKSERVTRAVATTFYRLLAVKDEYEVARLHTDAVF 1027 Query: 1008 RQQLEAQFEG----DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLR 1063 R+ LEAQFEG D+ ++F+LAP L + +P P K+ G W+ + G LAKF LR Sbjct: 1028 REALEAQFEGVAGKDFGIKFNLAPPTLTRPEP-GKNPVKKTFGQWMWPVLGTLAKFSSLR 1086 Query: 1064 GTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKE 1123 GT LDPFG +R++ER+L +YE T+ LA+L N +A L ++RGYG VK Sbjct: 1087 GTMLDPFGRTLERKMERELAGDYETTLQRALARLDAGNLEDVAKLADLHARVRGYGHVKL 1146 Query: 1124 RSIAKARQQEKLLREQL----AKGDEVQ 1147 ++A ++ E+ L +L A G+ V+ Sbjct: 1147 ANLAGVKRGERDLAARLQIEAATGESVR 1174 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: 2957 Number of extensions: 108 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: 1195 Length adjustment: 47 Effective length of query: 1109 Effective length of database: 1148 Effective search space: 1273132 Effective search space used: 1273132 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 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