Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2523 Length = 699 Score = 583 bits (1504), Expect = e-171 Identities = 316/697 (45%), Positives = 445/697 (63%), Gaps = 14/697 (2%) Query: 13 ELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIRE 72 ++ G V ++T+ + PVN L R+G++ + A+AD AV++++I GAG F GADI+E Sbjct: 6 KVHGSVAVITMANPPVNGLGLATRQGIVDGLGRANADAAVKSIVITGAGGAFSGGADIKE 65 Query: 73 FG--KPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPE 130 FG K P+L V IE KPVVAA+H A+GGGLE+AL HYRIA G + LPE Sbjct: 66 FGTDKSLQEPNLLSVIAAIENSAKPVVAAMHSVAMGGGLELALGCHYRIAAPGCSIALPE 125 Query: 131 VQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFG---LIDRLGSS-DDILA 186 V+LGL+PGAGGTQR PR+IG +AAL+LI+SG ++ A L D++ +S + + A Sbjct: 126 VKLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVKSEMIGAVPGQKLFDKMAASAESLAA 185 Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246 E LA+ + A P+ R+ A AR ++ +P K VDAVE Sbjct: 186 EALAFAQSVADAR-PLPLVRNFPCKHSEGD--AYFQFARNMVKGMAKNFPAPAKCVDAVE 242 Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGV 305 AA ++ F EG+ VER++F+ + +P+ L H F AER K P+ + P R + +GV Sbjct: 243 AATKKKFAEGMLVEREIFINLMWTPESRALRHLFMAERAASKIPDVASDTPKRDIKLVGV 302 Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365 +G GTMG GI++ L+AG+PV ++E +L RG A I+K Y+ + KG+L +K M Sbjct: 303 IGAGTMGGGISMNFLNAGIPVKILEMKQEALDRGVATIKKNYEAQVKKGKLKQDKYDQRM 362 Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425 + S + SYD DL+IEAVFE++ VK+AVF +LD V K GA+LA+NTS LD+D +A+ Sbjct: 363 ALLSTTLSYDDFKDCDLIIEAVFEEMGVKEAVFKQLDAVAKPGAILASNTSTLDVDKIAA 422 Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485 RP DV+G+HFFSPAN+MKLLEVV K+ + DV+AT + KK++KT V +GVCDGFI Sbjct: 423 FTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMAIGKKIKKTSVVSGVCDGFI 482 Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545 GNR++ Y A ++++G +P Q+D AV FGF MGPF++ DLAG DIGWA RKRR+ Sbjct: 483 GNRMIEQYSRQAGFLLDEGCTPQQVDKAVEKFGFAMGPFRMGDLAGNDIGWAIRKRRSVE 542 Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605 R +Y + AD+LCE G FGQK+G G+Y Y G R P V +I+ R GITPR Sbjct: 543 R-ADMKYSRTADKLCELGRFGQKTGAGWYDYQAGKRDAIPSDLVNKMIEDHRKELGITPR 601 Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665 +DEEI++R + A++NEGA+++ + IA + D+D+ +L GYGFP +RGGPM YA VGL Sbjct: 602 KISDEEIVQRLVFALVNEGAHILEDGIASKSGDIDMVYLTGYGFPIHRGGPMHYASEVGL 661 Query: 666 PKILADIREFAK---EDPLFWKPSPLLIELVERGADF 699 ++ + FA+ +D FWKP+PLL +L G F Sbjct: 662 FNVVQAMDRFARNPLDDAAFWKPAPLLAKLAAEGKAF 698 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: 1021 Number of extensions: 30 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: 699 Length adjustment: 39 Effective length of query: 667 Effective length of database: 660 Effective search space: 440220 Effective search space used: 440220 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