Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate PP_3282 PP_3282 3-hydroxyadipyl-CoA dehydrogenase
Query= SwissProt::P76083 (475 letters) >FitnessBrowser__Putida:PP_3282 Length = 505 Score = 397 bits (1019), Expect = e-115 Identities = 234/490 (47%), Positives = 300/490 (61%), Gaps = 29/490 (5%) Query: 4 NVQTVAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKLTA 63 NVQ VAVIG+G MGAGIA+VAA GH V LYD A +A+ GI +L V +GKL A Sbjct: 7 NVQ-VAVIGAGAMGAGIAQVAAQAGHPVKLYDNRPGAAAQAVTGIDRQLARLVDKGKLLA 65 Query: 64 ETCERTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTSSI 123 E RL PV + ALA A LVIEA E L+VK+ALF+QL +C +L +NTSS+ Sbjct: 66 AERETINARLCPVDTLEALADAGLVIEAIVENLQVKQALFSQLETLCAADCILASNTSSL 125 Query: 124 SITAIAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPVRC 183 SIT++AA ++ P+ V G+HFFNPAP+M LVEVVSGLAT V + +WGKQPV Sbjct: 126 SITSLAAGLERPQHVVGMHFFNPAPLMALVEVVSGLATDPAVAACIYATAQAWGKQPVHA 185 Query: 184 HSTPGFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDVNF 243 STPGFIVNRVARP+Y+E+ R L+E A +DA +RD GF MG ELTDLIG DVN+ Sbjct: 186 RSTPGFIVNRVARPFYAESLRLLQEGAADCASLDALMRDSGGFRMGAFELTDLIGHDVNY 245 Query: 244 AVTCSVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWR--------AEREAVVGL 295 AVTCSVF+AF+ + RF PSLVQ+ELV G LG+K+G G Y + AE + Sbjct: 246 AVTCSVFDAFYGDFRFQPSLVQKELVDAGHLGRKTGQGFYRYAEGVERPQPAELHSSACA 305 Query: 296 EA--VSDSFSPMK-------------VEKKSDGVTEIDDVLLIETQGETAQALA-----I 335 EA V + M+ ++ G+ ++ D L + G A A Sbjct: 306 EACVVEGNLGVMQPLVERLRQSGIAVTQRAGSGLIQVGDATLALSDGRLASQRAREDGLR 365 Query: 336 RLARPVVVIDKMAGKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVA 395 L + +D + + I+ +A DSA +A+ LQ+ G V +AD PG+++ RTVA Sbjct: 366 NLVLLDLALDYSSATRIAISWSADTSDSARDQAVALLQRAGLKVTGVADLPGLVVLRTVA 425 Query: 396 MIINEALDALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEE 455 M+ NEA DA+ +GV S DID AMR GVNYP GPLAW A +G LR+L+NLQ YGE Sbjct: 426 MLANEAADAVLQGVGSAADIDLAMRAGVNYPCGPLAWAANIGIAHTLRVLDNLQCSYGES 485 Query: 456 RYRPCSLLRQ 465 RYRP LLR+ Sbjct: 486 RYRPSLLLRR 495 Lambda K H 0.319 0.134 0.386 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: 546 Number of extensions: 19 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: 475 Length of database: 505 Length adjustment: 34 Effective length of query: 441 Effective length of database: 471 Effective search space: 207711 Effective search space used: 207711 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: 52 (24.6 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