Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate RR42_RS35145 RR42_RS35145 aldehyde dehydrogenase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Cup4G11:RR42_RS35145 Length = 514 Score = 417 bits (1072), Expect = e-121 Identities = 233/511 (45%), Positives = 316/511 (61%), Gaps = 6/511 (1%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L+++L G WQ+G G + + G+AL V + GLD+AA FA E+G ALRAMT+ E Sbjct: 5 LSNYLGGRWQAGSGAGATLSDPVLGDALVRVDATGLDLAAGFAFAREQGGAALRAMTYRE 64 Query: 64 RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122 RAAML A+ K L + ++ +Y ++ A +G DS VDI+GGI TL TYA LG L + Sbjct: 65 RAAMLAAIVKILQTNRDAYYEIATANSGTVHNDSAVDIDGGIFTLGTYAKLGDA-LGERR 123 Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182 + + L K+ F ++H+L GVA+ INAFNFP WG+ EK AP L G+P I+KP Sbjct: 124 YLIDGDAARLGKDPLFQSQHVLVPTRGVALLINAFNFPSWGLWEKAAPALLAGVPVIVKP 183 Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242 ATATA LTQ MV+ +VD+G++P GA+S++CGSA LLD L DVV+FTGSA T ++R Sbjct: 184 ATATAWLTQRMVRDVVDAGVLPPGALSVVCGSAAGLLDQLQPFDVVSFTGSAQTAALIRS 243 Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302 + +S+ +EADS+N +L F L +E REMT K+GQKCTAIRRI Sbjct: 244 HAAVTQRSVRVNIEADSVNSALLLPGEAAGSEAFDLLAKEAAREMTVKSGQKCTAIRRIF 303 Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362 VP+AL A +DA+ ARL +V VG+P E V+MGALV+ Q A V+E + L A + Sbjct: 304 VPEALYGAAADAIGARLARVTVGNPRHEAVRMGALVSRAQLASVREGLGYLQAQAEVLHD 363 Query: 363 GGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418 G L A PTLL VH TE FGPVATL+P ++ AL L Sbjct: 364 GATHALVDADPAVACCVGPTLLGARDAHAADRVHDTEVFGPVATLVPYRDNADALALVRR 423 Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478 G GSL +L +D + + A +HGR+ +++ + A+ TGHG+ +PQ +HGGPGRA Sbjct: 424 GQGSLVASLYGSDADALAKAAVELADSHGRVHVISPDVAQLHTGHGNVMPQSLHGGPGRA 483 Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAI 509 GGGEELGGLRA+ Y +R+AVQ S ++LA + Sbjct: 484 GGGEELGGLRALNFYHRRSAVQASTSVLAQL 514 Lambda K H 0.319 0.134 0.395 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: 814 Number of extensions: 28 Number of successful extensions: 4 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: 681 Length of database: 514 Length adjustment: 37 Effective length of query: 644 Effective length of database: 477 Effective search space: 307188 Effective search space used: 307188 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: 53 (25.0 bits)
Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate RR42_RS24800 RR42_RS24800 dehydratase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Cup4G11:RR42_RS24800 Length = 171 Score = 71.6 bits (174), Expect = 3e-17 Identities = 44/129 (34%), Positives = 74/129 (57%), Gaps = 8/129 (6%) Query: 531 FEELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSA 590 F+ELQ G + RT+TEAD+VN+ L+G+ H + A+++ FG+R+V G S Sbjct: 17 FDELQIGQVFRSGGRTVTEADVVNYCALTGNWIEIHSNTHYASKTRFGQRLVQGSLTYSI 76 Query: 591 AAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVE 650 GL + G+G + ANYG++++RF PV DTI C+ K+ +++ GV++ Sbjct: 77 VTGL-IQFGLG-IQANYGIDNMRFRNPVYINDTIYA--VCEVIGKKE----KDEKYGVIK 128 Query: 651 WAVEVFNQH 659 + + NQ+ Sbjct: 129 FRISAINQN 137 Lambda K H 0.319 0.134 0.395 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: 218 Number of extensions: 14 Number of successful extensions: 2 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: 681 Length of database: 171 Length adjustment: 28 Effective length of query: 653 Effective length of database: 143 Effective search space: 93379 Effective search space used: 93379 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: 49 (23.5 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