Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate RR42_RS24125 RR42_RS24125 hypothetical protein
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__Cup4G11:RR42_RS24125 Length = 1152 Score = 741 bits (1912), Expect = 0.0 Identities = 457/1183 (38%), Positives = 647/1183 (54%), Gaps = 70/1183 (5%) Query: 21 SLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWK 80 SL+ +Y + +++G QAL+R+ + Q D GL T F++GY GSPLG++D +L + Sbjct: 4 SLDARYEADTPLAFLNGNQALIRMIVEQMRSDGETGLRTKAFVTGYPGSPLGSIDIALRQ 63 Query: 81 AKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVF 140 AK+ L AH I +A NE+ A + + G+Q ++ +P +GV G WYGKGPG+DR+ D Sbjct: 64 AKRTLDAHGITHRAAQNEEFAVSMLSGTQMLDEHPHPDVDGVVGYWYGKGPGLDRSGDAL 123 Query: 141 KHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHA 200 KHAN AG+SRHG V++L+G+DH AKSST+ +Q E F+ G+PVLYP++VQE+LDYGLHA Sbjct: 124 KHANFAGTSRHGAVVILSGEDHEAKSSTVPYQQEFSFEHHGIPVLYPASVQEFLDYGLHA 183 Query: 201 WAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGG------LNIR-WP 253 A+SR+SG WV++K V + + V+L P + +P+ L GG N R +P Sbjct: 184 AALSRFSGCWVALKLVGTLCDGGEVVQLHPAGIRTQIPE---LQIGGKPFTRMANHRFFP 240 Query: 254 DPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGL 313 +E E RL D + A LAY RAN ++RI +P R GI++ GK++ DT+QAL +LG Sbjct: 241 VTNVETERRLYDERHAAVLAYARANGLNRIVRSAPGDRIGIISAGKSWADTQQALEDLGF 300 Query: 314 DDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDD 373 D GIRL KVG + P + R FAEGLQ I+V+EEKR +E + Sbjct: 301 DGPALQAQGIRLAKVGLLCPADGAFFREFAEGLQTIVVIEEKRDFLERQVAAGAVG--AT 358 Query: 374 VRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARI 433 VR ++ GK DE L P ++ ++A +A L + P R R Sbjct: 359 VR-EILGKHDE-----------HGQRLFPVEGGMTADMVAERLARILAR-STPLPERGR- 404 Query: 434 AARIAVIEAKEKAMAVPRVAA--ERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWM 491 RI +E +V R AA R P +CSGCPHN ST + G A GCH M Sbjct: 405 -ERIQYLEGN----SVKRDAALPGRAPNYCSGCPHNVSTLLAPGQMAWGAPGCHLFAALM 459 Query: 492 D---RSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNIT 548 D + +Q+GGEG+ W+G AP+ H+ N+GDG FHS IR +I G N+T Sbjct: 460 DKPQKRVEATTQLGGEGLPWLGLAPYTSRPHIVQNVGDGALFHSSYQNIRFAITTGANMT 519 Query: 549 YKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEV 608 +K+L N +A TGGQ G ++ D+A ++ +GA ++V+VT EP++Y A ++LP + Sbjct: 520 FKLLINGVLANTGGQEAVGASAIADLAGRLLQDGASRVVLVTKEPDQY-ARVQLPASLVR 578 Query: 609 HHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGD 668 D+L++ +EL + G TILIYD CA E+RRR+KRG P P +N+ VCE CGD Sbjct: 579 RSPDQLEQTMKELAAIKGVTILIYDGACANERRRRQKRGLLPAPTVFTVVNEEVCENCGD 638 Query: 669 CSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAE---GAQVKKPERHG 725 C K+NC+S++ + TE G K QI+QS+CN+D +C+ G CPSFVT E G V+KP Sbjct: 639 CGAKANCMSLQKVPTEFGPKTQIHQSTCNQDQACIQGECPSFVTVEVESGKGVRKPSLPA 698 Query: 726 VSMDNLPALPQPALPG-LEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGL 784 + ++P + PG L+ PY + + G+GG+GV+T +L AA ++ V D G Sbjct: 699 IDAASIPEIE----PGSLQAPYHIYIPGLGGSGVLTASAILAQAACMQGLQVKTYDQTGA 754 Query: 785 AQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVN 844 AQK GAVLS + +A H ++ +G+ADL + D + + + + TR +VN Sbjct: 755 AQKWGAVLSSLILAPADRPPHTNKVGIGKADLYLALDLLAAVETNNLKCCDANHTRVVVN 814 Query: 845 TAQTPTAEFIKNPKWQFPGLSAEQDVRNA-VGEACDFINASGLAVALIGDAIFTNPLVLG 903 P + I++ + P L + V A E+ ++A +A AL GD + TN + +G Sbjct: 815 AGVFPNGDVIRDSRKTLPTLELCETVAAAGRKESVLTLDARRIAEALFGDFMMTNMVAIG 874 Query: 904 YAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTG-KLRNTAEG 962 A+Q GWLP+ + + AI LNG VE N AF GR H PE V + KL A+ Sbjct: 875 AAYQAGWLPIRAECIEAAIGLNGAQVEANTMAFRAGRLWVHAPERVEVMGSLKLHPLADR 934 Query: 963 AEVVKLPTSSGAL----------------LEKLIAHRAEHLTAYQDAAYAQTFRDTVSRV 1006 E ++ S G L L + + R L YQ+ AYA + V+ Sbjct: 935 TERLRALRSEGKLKALARFESHLAKLSPQLRERVQLRFADLIDYQNTAYAARYLGRVTAS 994 Query: 1007 RAAESALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRD 1066 AE+A G G +T A A +L KLMAYKDEYEVARL T F ++ + F G Sbjct: 995 LQAEAAARGEGHGYEVTAAIAESLHKLMAYKDEYEVARLLTLSGFEKRVADMFSG----S 1050 Query: 1067 YQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTE 1126 +L + L PPL KG K R G LA LK LRG D F A R+ E Sbjct: 1051 VRLKYNLQPPLARTLGLKG---KLRVGGWIRPALKTLAALKFLRGTALDPFYALASRKEE 1107 Query: 1127 RALIGEYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVK 1169 RAL+ Y +L E + L A N A + L LP IRG+ VK Sbjct: 1108 RALLAWYEGVLGEGLKLLDAHNSAQVVELLRLPTTIRGYETVK 1150 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: 2868 Number of extensions: 123 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: 1197 Length of database: 1152 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1105 Effective search space: 1270750 Effective search space used: 1270750 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: 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