Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__BFirm:BPHYT_RS09560 Length = 694 Score = 681 bits (1758), Expect = 0.0 Identities = 363/693 (52%), Positives = 476/693 (68%), Gaps = 12/693 (1%) Query: 5 VTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGAD 64 V T D VA++T+++PPVN L + R GI+E V A DPA++AIVL AG+ F GAD Sbjct: 3 VDYTTHDGVAVITLNNPPVNGLGLSTRAGIVEGVERAQNDPAIKAIVLTGAGKAFSGGAD 62 Query: 65 ITEFGKPP--QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLG 122 ITEF P Q P L VI +E S KP IAAIH A+GGGLE+ALG H+R+A A++ Sbjct: 63 ITEFNTPKAGQEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIA 122 Query: 123 LPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGA 181 LPEVKLG+LPGAGGTQRLPRA+G E A+ MIV G+P+ + + GL +E+ + +L A Sbjct: 123 LPEVKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFDELAQGDLAEAA 182 Query: 182 VAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGA 241 +AFA+KV A++ P ++RD + A N VA M A+ AP C DA+ A Sbjct: 183 LAFARKVSAKEGPHPKVRDRKIEHPNAAGFIQFARNTVATM---AKNFPAPLKCIDAVEA 239 Query: 242 AIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAII 301 + F++GL ERE FM LV + +S A R+AFF ER A+K+ VP T R + +VA+I Sbjct: 240 GVQKGFDKGLAFERECFMALVQTPESHALRHAFFGERAASKIPDVPSDTPVRDIGQVAVI 299 Query: 302 GAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMA 361 GAGTMGGGIAM+F NAGIPVTL+ET +E L RGL ++KN+EAT +G L P+ +RMA Sbjct: 300 GAGTMGGGIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVLGQRMA 359 Query: 362 LITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAAT 421 LIT + +++K+ADLI+EAVFE + VK++ F +D AK GA+LASNTS L +D+IAA Sbjct: 360 LITPTLSYDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDVDKIAAF 419 Query: 422 TKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVG 481 TKRPQDV+GMHFFSPANVMKL E+VRG +TA D L T +++AKKI K VV GVCDGF+G Sbjct: 420 TKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGVCDGFIG 479 Query: 482 NRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK- 540 NRM+ +Q+ +L EGALP QVD + KFG MGPF M DLAG DIGW RK R ++ Sbjct: 480 NRMVEQYIRQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAIRKRRYLEH 539 Query: 541 -----SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDI 595 S+IAD LCE GRFGQKTG G+Y Y+ G R P V+ +I + +RR I Sbjct: 540 PDMHYSKIADRLCETGRFGQKTGGGWYDYKAGDRTAYPSKVVDDMIVAFSKETDTERRKI 599 Query: 596 TDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKH 655 +DEEI+ER+V+ ++NEGA+ILEE IA++ SDID+V+L GYG+P+YRGGPM YAD+VGL + Sbjct: 600 SDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLYADTVGLYN 659 Query: 656 IAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 + + YA N + + AP +A LAA+ + F Sbjct: 660 VERAIRRYAARPNGDAWQLAPSIAELAAKNRGF 692 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: 1123 Number of extensions: 52 Number of successful extensions: 7 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: 694 Length adjustment: 39 Effective length of query: 660 Effective length of database: 655 Effective search space: 432300 Effective search space used: 432300 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