Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate H281DRAFT_01671 H281DRAFT_01671 indolepyruvate ferredoxin oxidoreductase
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__Burk376:H281DRAFT_01671 Length = 1184 Score = 1151 bits (2977), Expect = 0.0 Identities = 609/1193 (51%), Positives = 791/1193 (66%), Gaps = 30/1193 (2%) Query: 8 PVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYR 67 PV + + VSL+DKY ERG Y+SG+ AL+R+ + QR RD AGLNTAGF+SGYR Sbjct: 4 PVIEVETAPTSEVSLDDKYRKERGYAYMSGSHALIRVMINQRIRDNDAGLNTAGFVSGYR 63 Query: 68 GSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYP-DARFEGVFGMW 126 GSPL D +LW A+ L H I F +NEDLAAT+VWG+QQ+ ++P ++ EGVF MW Sbjct: 64 GSPLAGFDTALWSAEAVLKQHQIKFLPAINEDLAATAVWGTQQLALFPQESTVEGVFSMW 123 Query: 127 YGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLY 186 YGKGPGVDR+ D KH N AG+S GGVLV A DDH AKSST HQSE A +PVLY Sbjct: 124 YGKGPGVDRSGDALKHGNGAGTSALGGVLVAAADDHTAKSSTFGHQSEQALIAAFIPVLY 183 Query: 187 PSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPG 246 P++VQ+YLD+G+ AM RYSGLW+ +KCV+DV+E+SA ++DPHR++I LP Sbjct: 184 PASVQDYLDFGVLGIAMGRYSGLWIGLKCVSDVIETSAVADVDPHRIDIRLPDKEFAADD 243 Query: 247 GLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQ 306 L+IR PD EQE R++ + A LA+ RAN+++ I I P ++ GIM GKAY D + Sbjct: 244 DLHIRSPDVWAEQEPRIVRKRLPAALAFCRANRLNSIRIKGPKSKLGIMCAGKAYNDVME 303 Query: 307 ALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEE 366 AL LGL D+ + G+ + K+G VWPL+ R FA GL E+LVVEEKR I+E +K+E Sbjct: 304 ALRLLGLSDDDIEKNGLAVLKIGMVWPLDPTILRDFAAGLDELLVVEEKRPIIEQQIKDE 363 Query: 367 LYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELP 426 LY+ + P V GGEW+ LL + YEL+P +A AI RL Sbjct: 364 LYSDALNGLPLVRVSGKGSGAIGGEWNRSGEACLLRSDYELTPVEVAGAIVARLRAQAGW 423 Query: 427 ADVRAR-IAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCH 485 + R R I AR+A +EA + AV A RKP+FCSGCPHNTST VPEGSRA AGIGCH Sbjct: 424 TETRKREIEARLAALEAVGRVQAV--AGAIRKPFFCSGCPHNTSTRVPEGSRATAGIGCH 481 Query: 486 YMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGV 545 YM MDR T +++ MGGEGV W+ QA F+ KH+FAN+GDGTYFHSG LAIR ++AA V Sbjct: 482 YMASSMDRRTESYTHMGGEGVPWVAQAQFSTRKHIFANIGDGTYFHSGSLAIRQAVAARV 541 Query: 546 NITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYS-AAIKLPQ 604 ++T+KILYNDA AMTGGQP+DG+L+V + QVAAEG R+I VV+D+ E+Y + Sbjct: 542 SMTFKILYNDAAAMTGGQPVDGELTVDGITRQVAAEGVRRIAVVSDDIEQYRISGTTFAA 601 Query: 605 GVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCE 664 G VH R ELD +QR LR+ G ++L+YDQTCA+EKRRRRK+GTYPDPAKR IN VCE Sbjct: 602 GTTVHDRSELDAVQRNLRDYEGVSVLVYDQTCASEKRRRRKKGTYPDPAKRVAINSEVCE 661 Query: 665 GCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQV------ 718 GCGDCSV+SNCLSVEPL+T LG KRQINQSSCNKDFSCV GFCPSFV+ EG ++ Sbjct: 662 GCGDCSVQSNCLSVEPLDTPLGRKRQINQSSCNKDFSCVQGFCPSFVSVEGGKLRSSQTK 721 Query: 719 KKPERHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTV 778 K PE M + P LP PA P + +L+ GVGGTGVVTIG LLGMAAHLE +G TV Sbjct: 722 KSPE---AMMADWPELPYPASPAMTDTVDILINGVGGTGVVTIGNLLGMAAHLEGRGCTV 778 Query: 779 LDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGR 838 LDMAGLAQKGGAV SHV++A+ ++++A+RI G AD++IGCD +V+A D +S+ + G+ Sbjct: 779 LDMAGLAQKGGAVWSHVRLASKRERMYASRIPSGSADVIIGCDLVVTAAPDTLSRIRKGK 838 Query: 839 TRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFT 897 TR ++N +PT+ F+ N WQ P + V + G + D+++A +A +GD +F+ Sbjct: 839 TRVVINGQTSPTSAFVANRDWQLPEAELKSHVESVCGDDFVDWVDAQEIARRHLGDTVFS 898 Query: 898 NPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLR 957 N ++LG+ WQ+G +PL+ +++ RAIELNG AV+KNK AF GR +A +P + Sbjct: 899 NAIMLGFVWQQGLIPLARESIERAIELNGQAVKKNKLAFQIGRWLAVNP-------ARFA 951 Query: 958 NTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNG 1017 E V+ +L++LI R L AYQ YA+ + VS + A + +G Sbjct: 952 AGEEVESVIVWRQKKKVVLDELIQSRVSLLAAYQSERYAREYETFVSEITAQVGS---HG 1008 Query: 1018 KPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPL 1077 K A A L KLMAYKDEYEVARLY+ P F L NQFEG D+++ ++LAPP+ Sbjct: 1009 KREAFILAVAEGLYKLMAYKDEYEVARLYSLPGFKKSLENQFEG----DFKIRYYLAPPM 1064 Query: 1078 MAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALL 1137 +++++EKG L+K+ FGP +F +LA+LK LRG FD FG TAERR ERALI EYR + Sbjct: 1065 LSRKNEKGELIKKEFGPWLGHVFPLLARLKILRGTPFDPFGHTAERRRERALIREYRLWI 1124 Query: 1138 EELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHP 1190 L A I LA LPD IRG+GHVK+ + +V + LL P Sbjct: 1125 RTALTHL-ADKPDVCIELAKLPDSIRGYGHVKERAIDEVMAKRDTLLAALSAP 1176 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: 3254 Number of extensions: 138 Number of successful extensions: 12 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: 1184 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1137 Effective search space: 1307550 Effective search space used: 1307550 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