Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate RR42_RS35270 RR42_RS35270 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Cup4G11:RR42_RS35270 Length = 693 Score = 583 bits (1503), Expect = e-171 Identities = 322/696 (46%), Positives = 434/696 (62%), Gaps = 12/696 (1%) Query: 9 VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68 V + G++ ++T++ PVNALSA VR G+LA IE A AD V +++ AG+ FIAGA Sbjct: 7 VADLAVEGEIAILTLNSPPVNALSAAVRAGILAGIERAIADSNVRGIVLTCAGKTFIAGA 66 Query: 69 DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128 DI EFGKPPV PSL DV IE KPVVAAIHG ALGGGLEVAL HYR+A A+ GL Sbjct: 67 DITEFGKPPVGPSLADVQAAIEGSPKPVVAAIHGTALGGGLEVALVCHYRVAARSARCGL 126 Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG 188 PEV LGLLPGAGGTQR PR++G ALD++ SG H A A GL D + + A Sbjct: 127 PEVNLGLLPGAGGTQRLPRIVGPAKALDMVTSGAHIGAAAAAEMGLFDLVTEDAALRASA 186 Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAV-ATARAETAKKSRGLFSPLKIVDAVEA 247 +A+ ++ A P+R+ RD + A + A R A+K RG +P + +EA Sbjct: 187 IAFARQVNAEQRPLRKVRDLNEKVEAARGKPELFADFRRANARKFRGFDAPEYNIRCIEA 246 Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVV 306 A+ PFDEG++VERKLFLE ++ Q A + FFA R+V P+ A P + +G++ Sbjct: 247 AVNLPFDEGMKVERKLFLELMNGTQSAAQRYYFFASRQVWNVPDVPADTPVIDVKKVGII 306 Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366 G GTMG GIA+ +L+AG+PV ++E +L RG I YD KGR++A M+ Sbjct: 307 GAGTMGGGIAMNMLNAGIPVVIVETAQQALDRGVRTIRANYDNTAKKGRITAADVDRRMA 366 Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426 + + LA ADLVIEAV+E++ VK+ +F +LD++ K GA+LATNTS LD++ +A + Sbjct: 367 LLTPTLELGQLADADLVIEAVYENMDVKKDIFGKLDKIVKPGAILATNTSALDVNEIARA 426 Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486 SRP VIGLHFFSPAN+MKLLEVV + + V+ T+ ELA+K+ K GVC GF+G Sbjct: 427 TSRPESVIGLHFFSPANVMKLLEVVRGDKTAKPVIRTSMELARKIGKIAALVGVCPGFVG 486 Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546 NR+LA + A ++ +GA P+ ID + FGFPMGPF + DLAG D+GW K +AT Sbjct: 487 NRMLAQRQREAQKLVLEGALPWDIDRVLYNFGFPMGPFAMSDLAGLDLGWIREKSSSAT- 545 Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606 + + LCE GQK+G G+Y Y E R+ P P VE II AR G T R Sbjct: 546 --------LREILCEMDRRGQKTGAGYYDYDE-KRNAIPSPVVEGIIRDFAARQGKTSRV 596 Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666 ++EI+ R + MINEGA ++ E A+R D+DV ++ GYG+P YRGGPM YAD +GL Sbjct: 597 VCEQEILERCIYPMINEGAKILEEGKAIRASDIDVVWVNGYGWPVYRGGPMCYADTIGLD 656 Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADFASL 702 K+LA ++ F +KP+ LL +LV +G F+ L Sbjct: 657 KVLAVMKNFEATLGADFKPARLLEDLVAQGKKFSDL 692 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: 1100 Number of extensions: 68 Number of successful extensions: 6 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: 693 Length adjustment: 39 Effective length of query: 667 Effective length of database: 654 Effective search space: 436218 Effective search space used: 436218 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