Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_012968361.1 KVAR_RS14350 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::P76083 (475 letters) >NCBI__GCF_000025465.1:WP_012968361.1 Length = 473 Score = 679 bits (1751), Expect = 0.0 Identities = 346/474 (72%), Positives = 393/474 (82%), Gaps = 2/474 (0%) Query: 1 MMINVQTVAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGK 60 M ++ TVAVIGSGTMGAGIAEVAA+ GH VL+YDI +A+ RAIDGI RL SRV RGK Sbjct: 1 MTTSLATVAVIGSGTMGAGIAEVAAAAGHPVLIYDIDHQAIARAIDGIARRLASRVERGK 60 Query: 61 LTAETCERTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNT 120 L +E + L RL P D+ ALA ADLVIEAASERLEVK ALFAQLA +C P TLLT+NT Sbjct: 61 LASEQADALLARLHPAHDLAALADADLVIEAASERLEVKTALFAQLAAICAPSTLLTSNT 120 Query: 121 SSISITAIAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQP 180 SSISITAIAA +KNPERVAGLHFFNPAPVMKLVEVVSGL T+AEVVEQLC+ WGKQP Sbjct: 121 SSISITAIAAGVKNPERVAGLHFFNPAPVMKLVEVVSGLETSAEVVEQLCQCVSGWGKQP 180 Query: 181 VRCHSTPGFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQD 240 VRC STPGFIVNRVARP+Y+EAWRALEEQVAAPEVIDAALRDG GFPMGPL LTDLIGQD Sbjct: 181 VRCRSTPGFIVNRVARPFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQD 240 Query: 241 VNFAVTCSVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWRAEREAVVGLEAVSD 300 VNFAVTCSVFNAFWQ+RR+LPSL+QQEL + GRLGKKSG GVY W AE L V++ Sbjct: 241 VNFAVTCSVFNAFWQDRRYLPSLLQQELALAGRLGKKSGYGVYRWPAETLPDAALPPVAN 300 Query: 301 SFSPMKVEKKSDGVTEIDDVLLIETQGETAQALAIRLARPVVVIDKMAGKVVTIAAAAVN 360 V SD VTE+D++LL+ET+GETA AL+++ RPVVV D A V +AAAA N Sbjct: 301 --GAQSVMTISDSVTELDELLLLETEGETALALSVKHHRPVVVYDLCASDTVVLAAAATN 358 Query: 361 PDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVAMIINEALDALQKGVASEQDIDTAMR 420 + T KA++Y QQQGK VL+IADYPG+L+WRTVAM+INEALDALQKG+AS QDIDTAMR Sbjct: 359 APAVTDKAVHYFQQQGKKVLRIADYPGLLVWRTVAMLINEALDALQKGIASPQDIDTAMR 418 Query: 421 LGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEERYRPCSLLRQRALLESGYE 474 LGVNYP+GPLAWG +LGW+R+L+LLENLQHHYGEERYRP SLLRQ+AL+E +E Sbjct: 419 LGVNYPHGPLAWGERLGWRRVLQLLENLQHHYGEERYRPSSLLRQKALMEKHHE 472 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: 663 Number of extensions: 20 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: 475 Length of database: 473 Length adjustment: 33 Effective length of query: 442 Effective length of database: 440 Effective search space: 194480 Effective search space used: 194480 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: 51 (24.3 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