Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate CCNA_03293 CCNA_03293 multifunctional fatty acid oxidation complex subunit alpha FadJ
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Caulo:CCNA_03293 Length = 696 Score = 589 bits (1519), Expect = e-172 Identities = 319/693 (46%), Positives = 438/693 (63%), Gaps = 12/693 (1%) Query: 9 VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68 V + G + +VT++ PVNALSA VR GL A +AA AD AV+A++++ G+ FIAGA Sbjct: 11 VTDFSVEGDIGVVTLNSPPVNALSAAVREGLQGAFDAAIADAAVKAIVLICDGKTFIAGA 70 Query: 69 DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128 DI EFGK PSL DV N IE KPV+AAIHG ALGGGLEVAL A+YR+AV AK GL Sbjct: 71 DITEFGKAMTGPSLQDVQNVIENSPKPVIAAIHGTALGGGLEVALVANYRVAVPSAKAGL 130 Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG 188 PEV +GLLPGAGGTQR PR++G + AL+++ +G+H AK A A GL D L + Sbjct: 131 PEVNIGLLPGAGGTQRLPRIVGVEKALEMVTTGQHVPAKAAHAMGLFDELVEEGKLREGA 190 Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATA-RAETAKKSRGLFSPLKIVDAVEA 247 +A+ ++A + P+++ RD + A + A R AKK RG +P + +EA Sbjct: 191 IAFAKAVVAENRPLKKVRDLNEKVEAARGKPEIFEAFRKANAKKFRGFMAPENNIKCIEA 250 Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVV 306 A+ PFDEGL+ ERKLF+E + Q A + FFAER+ K P+ P + +GV+ Sbjct: 251 AVNLPFDEGLKAERKLFMELMTGSQSAAQRYVFFAERQAAKIPDVPDDTPTIPVKKVGVI 310 Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366 G GTMG GIA+ L+AG+PVT+IE +L RG I K Y+ KGRL+ + M+ Sbjct: 311 GAGTMGGGIAMNFLNAGIPVTIIEAKQENLERGVGIIRKNYENTAKKGRLTQDDVEKRMA 370 Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426 + S +ALA D++IEAVFE + +K+ VF +LD++ K GA+LATNTSYLD+DA+A+ Sbjct: 371 LLTPSMEMEALADCDMIIEAVFELMEIKKEVFTKLDKIAKPGAILATNTSYLDVDAIAAV 430 Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486 SRP VIG HFFSPAN+M+LLE+V + S DV+AT +L+K + K PV GVC GF+G Sbjct: 431 TSRPESVIGTHFFSPANVMRLLELVRGDKTSKDVIATCMKLSKTIGKVPVLVGVCYGFVG 490 Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546 NR+LA + A ++ +GA P+ +D + FG PMGPF + DLAG DIGW K ++T Sbjct: 491 NRMLAQRQREAQKLILEGAMPWDVDRVLYDFGLPMGPFAMSDLAGLDIGWDPAKTSSST- 549 Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606 + + LCE GQK+G+GFY Y E +R+ P P VE +I + I R Sbjct: 550 --------VREVLCEMDRRGQKNGKGFYDYDE-NRNAKPSPVVEEVIRDFAEKRQIQRRE 600 Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666 TD+EI+ R + M+NEGA ++ E A+R D+D+ ++ GYG+P Y GGPM + ++VGL Sbjct: 601 ITDQEILERCLYPMVNEGAKILEEGKAIRASDIDIVWINGYGWPVYSGGPMFWGELVGLD 660 Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADF 699 K+LA +++F E +KPS LL LV G F Sbjct: 661 KVLAKMKQFHAELGDDFKPSALLERLVAEGKGF 693 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: 1053 Number of extensions: 52 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