Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_034210667.1 N787_RS02965 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_000747155.1:WP_034210667.1 Length = 680 Score = 267 bits (683), Expect = 1e-75 Identities = 209/669 (31%), Positives = 316/669 (47%), Gaps = 48/669 (7%) Query: 11 DQVAIVTVDSPP--VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68 D + ++T+D VNALS AV + V + +++ FI GADI F Sbjct: 21 DGILVLTLDRADQNVNALSRAVLDELESMVERIALELPKGVVIISGKAAGFIPGADIKGF 80 Query: 69 GKPPQPPALND-------VIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK- 120 G D V L PT+AAIHG +GGG E++L C +R+A + K Sbjct: 81 GDIAAKGQTEDWIRHGQLVFQKLAELRCPTVAAIHGHCMGGGTEISLACRYRIASNDEKT 140 Query: 121 -LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVA 179 +GLPEVKLG+ PG GG+ R PR +G A+ +++ G + A+ A GLV++VV A Sbjct: 141 RIGLPEVKLGIYPGWGGSVRAPRLLGAPAAMDLMLTGRSLSASAARAIGLVDKVV----A 196 Query: 180 GAVAFAKKV-LAEKRPLRRLRDDDSKLAAAKAD-RSIFTNAVAA-MTKKARG--LEAPFA 234 AV + V LA++ R + A R++ +A + +KAR APFA Sbjct: 197 PAVLLDEAVKLAQRGTTRPFKQRFLAWATNTGPGRALLAPQIAKQVARKARKEHYPAPFA 256 Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294 + + LP LK E + +KL + + FF + G G Sbjct: 257 LIETWRRSGGLPVHAALKAEAKSVVKLAATPTAHNLVRVFFLMDRLKSLGGKDHG----- 311 Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354 +S+V +IGAG MGG IA A G VTL + + ++ L K +E Sbjct: 312 ISKVHVIGAGVMGGDIAAWCALRGFEVTLQDREMKYIQPALDRAAKLFEKKVKDEAKRAA 371 Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414 A+ A + G V DADL+IEA+FE + K+ +F V+ KPGA+L SNTS + Sbjct: 372 TSARLKADVEGT----GVADADLVIEAIFENLEAKQALFAKVEETLKPGAILVSNTSSIP 427 Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474 + ++ A K P G+H+F+P +M L EIVR + + K I K+PV V Sbjct: 428 LTDLRAGRKDPARFAGLHYFNPVALMPLVEIVRHDGLDAETERRLAAFCKAIDKLPVPVA 487 Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534 GF+ NR+LA +++ EG +D V KFGMPMGP + D GLD+ Sbjct: 488 GTPGFLVNRILAPYMQEAIVAFSEGIPGPVIDKVALKFGMPMGPIELVDTVGLDVAASVG 547 Query: 535 KDRG--IKSEIADAL-CEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLK 591 K + DA E G+ G+K G+G YK+E G RA P+ + Sbjct: 548 KIMADFHGQPLPDAFKVEDGKRGKKDGQGLYKWENG-RAVKPE---------------VP 591 Query: 592 RRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSV 651 + E++ +R++ P++NE L + + + +D ++G G+ +RGGP+ + +V Sbjct: 592 KDYQAPEDLEDRLILPLLNEAVSCLHDGVVSDADLLDAGVIFGTGFAPFRGGPIQHIKAV 651 Query: 652 GLKHIAERL 660 G + RL Sbjct: 652 GADKLKARL 660 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: 1094 Number of extensions: 61 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: 680 Length adjustment: 39 Effective length of query: 660 Effective length of database: 641 Effective search space: 423060 Effective search space used: 423060 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