Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate RR42_RS22630 RR42_RS22630 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Cup4G11:RR42_RS22630 Length = 696 Score = 658 bits (1697), Expect = 0.0 Identities = 355/692 (51%), Positives = 472/692 (68%), Gaps = 16/692 (2%) Query: 10 QDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFG 69 Q ++AI+ +D+PPVN L VR G+ + + A D AV AIV++ AG+ F GADI +F Sbjct: 9 QGRIAILLLDNPPVNGLGDTVRLGLFDGIAQATQDDAVAAIVILGAGKVFCGGADIRQFN 68 Query: 70 KPPQP--PALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVK 127 P P L VIA +E S KP +AAIHG ALGGG+E+ALGCH+R+A +A LGLPEV Sbjct: 69 APAASAQPTLRQVIARIEQSAKPVVAAIHGVALGGGMELALGCHYRIASADASLGLPEVN 128 Query: 128 LGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAFAK 186 LGL+PG GGTQRLPR +G A+++I GG P+ +A+ G+ + +++ + +A A+AFA+ Sbjct: 129 LGLVPGGGGTQRLPRLIGVPAALELIQGGKPVRGDKAVALGMADALIDGDPLAAAMAFAE 188 Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246 +V L ++ A A F AA++ KAR A A + AA LP Sbjct: 189 RVAG----LPGAHPVIARRPCADAAGVDFAARSAAVSAKARNALAQRAAIACVQAATRLP 244 Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306 + GL ER F +LV S +SKA R+ FFAEREA KV +P G R V+RV I+GAGTM Sbjct: 245 IDAGLDDERARFDQLVASTESKALRHLFFAEREAPKVAALPAGASLRTVARVGILGAGTM 304 Query: 307 GGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGL 366 G GIAM+FANAGI VTL+E + L RGL ++++N+E TAA+G L A+RMA IT Sbjct: 305 GAGIAMAFANAGIAVTLLEQQQAALDRGLAMIRRNYEITAAKGKLTAQEIAQRMACITPT 364 Query: 367 VGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQ 426 + + DADL+IEAVFE MAVKK VF +DA KPGA+LA+NTS LSID IAA+T RPQ Sbjct: 365 LADAALADADLVIEAVFEDMAVKKAVFARLDALCKPGAILATNTSRLSIDVIAASTSRPQ 424 Query: 427 DVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLA 486 DV+G+HFFSPANVMKL E+V+G +TAP+ + T + +A+ I K+PV+V VC+GFVGNRML Sbjct: 425 DVIGLHFFSPANVMKLLEVVQGERTAPEVIATCMKMARAIGKIPVLVRVCEGFVGNRMLT 484 Query: 487 ARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK------ 540 +++ LL EGA PQQVD +T+FGM MGP AM DLAG+DI W +RK Sbjct: 485 PYWREAGFLLEEGASPQQVDGALTRFGMAMGPLAMADLAGMDINWATRKRLAPTRPAHLR 544 Query: 541 -SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599 S++AD +CE GRFGQKT GYY+YE GSRAP+PDP V+ LI A+ G++RR+++DEE Sbjct: 545 YSKVADRICEQGRFGQKTNAGYYRYEAGSRAPLPDPAVDALIRACAAEAGIERREVSDEE 604 Query: 600 ILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAER 659 I+ER + + NEGARILEE IA R +DIDVV+++GYG+P +RGGPM +A+++GL E+ Sbjct: 605 IVERCMLALANEGARILEEGIARRAADIDVVYVHGYGFPAWRGGPMFHAETIGLGRTLEK 664 Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGK-TFAS 690 + A A + PAPLL RL A+G+ TFA+ Sbjct: 665 IRA-LNAIHGEHWTPAPLLVRLVAQGRETFAA 695 Lambda K H 0.317 0.134 0.383 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: 1160 Number of extensions: 50 Number of successful extensions: 5 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: 699 Length of database: 696 Length adjustment: 39 Effective length of query: 660 Effective length of database: 657 Effective search space: 433620 Effective search space used: 433620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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