Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate RR42_RS22630 RR42_RS22630 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Cup4G11:RR42_RS22630 Length = 696 Score = 603 bits (1554), Expect = e-176 Identities = 337/692 (48%), Positives = 443/692 (64%), Gaps = 17/692 (2%) Query: 15 RGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFG 74 +G++ ++ +D+ PVN L VR GL I A D AV A++I+GAG+ F GADIR+F Sbjct: 9 QGRIAILLLDNPPVNGLGDTVRLGLFDGIAQATQDDAVAAIVILGAGKVFCGGADIRQFN 68 Query: 75 KPPVP--PSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQ 132 P P+L V RIE KPVVAAIHG ALGGG+E+AL HYRIA A LGLPEV Sbjct: 69 APAASAQPTLRQVIARIEQSAKPVVAAIHGVALGGGMELALGCHYRIASADASLGLPEVN 128 Query: 133 LGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYV 192 LGL+PG GGTQR PRLIG AAL+LI G+ +A+A G+ D L D LA +A+ Sbjct: 129 LGLVPGGGGTQRLPRLIGVPAALELIQGGKPVRGDKAVALGMADALIDGDP-LAAAMAFA 187 Query: 193 HE---LLAAHAPVRRT--RDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247 L AH + R DAA + A S A A AR A+++ + V+A Sbjct: 188 ERVAGLPGAHPVIARRPCADAAGVDFAARSAAVSAKARNALAQRAA--------IACVQA 239 Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVV 306 A P D GL ER F + + S + L H FFAERE K A A RT+ +G++ Sbjct: 240 ATRLPIDAGLDDERARFDQLVASTESKALRHLFFAEREAPKVAALPAGASLRTVARVGIL 299 Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366 G GTMGAGIA+A +AG+ VT++E+ A+L RG A I + Y+ AKG+L+A++ A M+ Sbjct: 300 GAGTMGAGIAMAFANAGIAVTLLEQQQAALDRGLAMIRRNYEITAAKGKLTAQEIAQRMA 359 Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426 + + + ALA ADLVIEAVFED+AVK+AVFA LD +CK GA+LATNTS L ID +A+S Sbjct: 360 CITPTLADAALADADLVIEAVFEDMAVKKAVFARLDALCKPGAILATNTSRLSIDVIAAS 419 Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486 SRP DVIGLHFFSPAN+MKLLEVV ++ + +V+AT ++A+ + K PV VC+GF+G Sbjct: 420 TSRPQDVIGLHFFSPANVMKLLEVVQGERTAPEVIATCMKMARAIGKIPVLVRVCEGFVG 479 Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546 NR+L Y A ++E+GASP Q+D A+ FG MGP + DLAG DI WA RKR A TR Sbjct: 480 NRMLTPYWREAGFLLEEGASPQQVDGALTRFGMAMGPLAMADLAGMDINWATRKRLAPTR 539 Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606 RY ++ADR+CE+G FGQK+ G+Y Y GSR+ PDP V+A+I A A AGI R Sbjct: 540 PAHLRYSKVADRICEQGRFGQKTNAGYYRYEAGSRAPLPDPAVDALIRACAAEAGIERRE 599 Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666 +DEEI+ R M A+ NEGA ++ E IA R D+DV +++GYGFP +RGGPM +A+ +GL Sbjct: 600 VSDEEIVERCMLALANEGARILEEGIARRAADIDVVYVHGYGFPAWRGGPMFHAETIGLG 659 Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGAD 698 + L IR W P+PLL+ LV +G + Sbjct: 660 RTLEKIRALNAIHGEHWTPAPLLVRLVAQGRE 691 Lambda K H 0.320 0.136 0.392 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: 1143 Number of extensions: 53 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: 706 Length of database: 696 Length adjustment: 39 Effective length of query: 667 Effective length of database: 657 Effective search space: 438219 Effective search space used: 438219 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: 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