Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate GFF4162 Psest_4235 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__psRCH2:GFF4162 Length = 701 Score = 206 bits (524), Expect = 3e-57 Identities = 147/398 (36%), Positives = 222/398 (55%), Gaps = 30/398 (7%) Query: 5 VIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKE-GVEQV 63 VIG G MG GIA A AG V + +I+ E LQ+ ++R + + + + GSL E +EQ Sbjct: 300 VIGGGTMGVGIALSFANAGVPVKLLEINEEALQRGLQRARDTYAASVKRGSLTEDAMEQR 359 Query: 64 LARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISEI 123 LA I T+ A AL +D V+EAV E++ +K+ +F +A P A+LA+NTSSL + I Sbjct: 360 LALIEGVTEYA-ALADADVVVEAVFEEMGVKQQVFEQLDAICKPGAILASNTSSLDLDAI 418 Query: 124 ASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVPG 183 A+ K P+ VVG+HFF+P +M L+E+VRG TSDEV+ T + K + K ++VV G Sbjct: 419 AAFTKRPEDVVGLHFFSPANVMRLLEVVRGAKTSDEVLATAMAIGKQLKKVSVVVGVCDG 478 Query: 184 FFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK- 242 F NR++ + +L+E+G A+ Q+VD +A+ G MG F + D +GLDIG ++ K Sbjct: 479 FVGNRMVFQYGREAEFLLEEG-ATPQQVD-AALRNFGMAMGPFAMRDLSGLDIGQAIRKR 536 Query: 243 -AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY------PSPGKFVRPTLPSTSKKL 295 T FP S +KL + G LG K+G+GYY+Y P + P L + S + Sbjct: 537 QRATLPAHLDFPTVS-DKLCAAGMLGQKTGAGYYRYEPGNRTPQENPDLAPMLEAASLEK 595 Query: 296 G--------RYLIS----PAVNEVSYLLREGIVGK-DDAEKGCVLGLGLPK---GILSYA 339 G +Y++ VNE + +L EGI + D + + G G P G + YA Sbjct: 596 GIERKALDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAFRGGPMFYA 655 Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 D +G+D V+ ++E+ G D + P PLL + EG+ Sbjct: 656 DSVGLDRVLARVKELHARCG-DWWKPAPLLEKLAAEGR 692 Score = 124 bits (311), Expect = 1e-32 Identities = 85/228 (37%), Positives = 126/228 (55%), Gaps = 20/228 (8%) Query: 398 TIVVRVEPP--LAWIVLNRPTRYNAINGDMIRE-INQALDSLEEREDVRVIAITGQGRVF 454 T VVR+E +A I +N P NA+ G +RE + +A S E VR +A+ +G F Sbjct: 2 TDVVRLEVQGEIALITVNNPP-VNAL-GQAVREGLQKAFQSAEADPQVRAVALVCEGNTF 59 Query: 455 SAGADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFR 514 AGAD+ EFG ++ EV I+ K +AVI+G ALGGG+E+AL +R Sbjct: 60 IAGADIKEFGKPPQAPSL------PEVIEIIEACNKSSVAVIHGTALGGGLEVALGCHYR 113 Query: 515 VASKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFL 573 +A K A++G PE+ LGL+PG GGTQRL RL+G K LE++++G+ + A EA IV+ L Sbjct: 114 IARKDAKVGLPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPISAAEAVEHNIVDEL 173 Query: 574 AEPEELESEVRKLANAIAEKSPLAVASAKLAYKLGEETHIWTGTSLEA 621 E + +E+ + + + E + + GE+T G EA Sbjct: 174 FEGDLVEAGLAYVRRMVEE--------GRTPRRTGEQTQGLEGADNEA 213 Score = 26.9 bits (58), Expect = 0.003 Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 3/95 (3%) Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354 +G ++ E +LL EG + + G+ G + D G+D+ + Sbjct: 480 VGNRMVFQYGREAEFLLEEGATPQQ--VDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQ 537 Query: 355 RQTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTY 389 R T H + + G LG+K+G G++ Y Sbjct: 538 RATLPA-HLDFPTVSDKLCAAGMLGQKTGAGYYRY 571 Lambda K H 0.316 0.134 0.377 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: 922 Number of extensions: 49 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 651 Length of database: 701 Length adjustment: 39 Effective length of query: 612 Effective length of database: 662 Effective search space: 405144 Effective search space used: 405144 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 (21.6 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