Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_066599254.1 V473_RS00615 hypothetical protein
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_001046645.1:WP_066599254.1 Length = 689 Score = 506 bits (1302), Expect = e-147 Identities = 297/693 (42%), Positives = 412/693 (59%), Gaps = 26/693 (3%) Query: 13 VAIVTVDSPPVNALSAA--VRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF-G 69 V +V D+ PVNAL+ + + I V A D V AI+L G F AGADI +F G Sbjct: 11 VLVVRFDNSPVNALTVGGGLVQAIERRVAQAQTDERVDAIILTGGGTVFSAGADIADFEG 70 Query: 70 KPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLG 129 P + A+ ++ ++EN KP +AAI G LGGGLE+AL HFRVA AK G PE+ LG Sbjct: 71 APERIDAIRSLMQSIENCRKPVVAAIEGLCLGGGLELALAAHFRVASSTAKFGFPEISLG 130 Query: 130 LLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAF--AK 186 LLPG GGTQR PR G A+ +++ G + AA+AL+ GL++ + E ++V A+A A Sbjct: 131 LLPGGGGTQRSPRLAGAGNAIDLMLSGKSVSAAKALEIGLIDRIAEGDVVEAALAMLAAG 190 Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246 V + +R D A A+R +T R + AC AI A DL Sbjct: 191 LVGSTRRSGSLPVPQDLDAAIDSAERR------TGLTDAGRAI---IACVRAI-AQTDL- 239 Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306 + GLK E E F L+ S+QS+A R+AFF R K+ G + + V V ++G G M Sbjct: 240 -QAGLKLEAEQFGALMTSEQSRALRHAFFGRRIVGKIPGGVR-VESKGVRHVTVVGGGLM 297 Query: 307 GGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGL 366 G GIA+S NA + VT++E E + ++ + A + + +R+ + Sbjct: 298 GTGIAISLLNADLGVTVVEAKPEGFDKCRASIEASLRRDADKARITAATADRRIGALNMG 357 Query: 367 VGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQ 426 ++ +DL IEAVFE M K+EVF A+D A GA+LASNTS L +D IA T RP+ Sbjct: 358 RSIDEAMPSDLYIEAVFEDMDAKREVFQALDRIAPLGAILASNTSTLDLDAIAQFTSRPE 417 Query: 427 DVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLA 486 V+G+HFFSPAN+M+L E+VRGA+T+P+ L +A++ AK I K VV GVCDGF+GNR+ Sbjct: 418 AVVGLHFFSPANIMRLLEVVRGARTSPETLASAMAFAKSIGKTGVVAGVCDGFIGNRIFE 477 Query: 487 ARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK------ 540 +Q+ LL EGALP Q+DA + FGM MGP + DLAG DIGW RK R ++ Sbjct: 478 EYLRQAWFLLEEGALPHQIDAALEAFGMAMGPCRVMDLAGQDIGWNIRKRRAVEQPDRPY 537 Query: 541 SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEI 600 S+I D +CE GRFGQKTG G+Y Y G R P DP +E LI ++ RR I D EI Sbjct: 538 SKIPDLVCELGRFGQKTGTGFYLYPDG-RTPQRDPLIEALIVSHSRQIDFDRRVIDDSEI 596 Query: 601 LERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERL 660 +ER ++ MINEGA+++ E IA RP D+D+++L GYG+P RGGPM +AD VGL H+ E++ Sbjct: 597 VERCIFAMINEGAKLVGEGIAYRPVDVDIIYLDGYGFPASRGGPMFHADQVGLPHLLEKM 656 Query: 661 SAYAKATNDPSLEPAPLLARLAAEGKTFASLTQ 693 + YA+ + + EPAPL+ L+ + + F L + Sbjct: 657 AQYARGHHGWAWEPAPLILELSDKNQKFGDLNR 689 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: 1086 Number of extensions: 50 Number of successful extensions: 6 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: 689 Length adjustment: 39 Effective length of query: 660 Effective length of database: 650 Effective search space: 429000 Effective search space used: 429000 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 24 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