Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Korea:Ga0059261_0837 Length = 676 Score = 562 bits (1449), Expect = e-164 Identities = 316/691 (45%), Positives = 427/691 (61%), Gaps = 22/691 (3%) Query: 10 VSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGAD 69 ++ E +G +L++T ++ PVNAL A VR+GL AAI+ D +++A +I GR F AGAD Sbjct: 5 ITTERQGDILVITSNNPPVNALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFFAGAD 64 Query: 70 IREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLP 129 I EFGKP PSLP + + IEA KPVVAA+HG ALGGG EVALA HYRIAV AK GLP Sbjct: 65 ITEFGKPMQEPSLPVLVDLIEASEKPVVAAVHGTALGGGCEVALACHYRIAVPSAKFGLP 124 Query: 130 EVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGL 189 EV+LG+LPGAGGTQR PR+ G + AL+L G SA A GL+DRL D + A+ + Sbjct: 125 EVKLGILPGAGGTQRLPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAGEDSLTADAI 184 Query: 190 AYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAI 249 AY +E+ AA P+ RT + + A R AK+ R + +P +I+ +E Sbjct: 185 AYANEIAAAR-PLPRTSEKPVTVEAGVFEAF----RKTNAKRFRNMDAPAEIIAVIEETA 239 Query: 250 EQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPET-RAAKPRTLNTIGVVGG 308 +P+ EG++ ER F++ I Q A L H FFAER+ K + K R + +GV+G Sbjct: 240 GKPYAEGVQRERMGFMKLIMGAQSAALRHIFFAERKAAKIDDVPEDTKLRPIKRVGVIGA 299 Query: 309 GTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRW 368 GTMG GI++ L AG+PVT+ E +L RG I K Y+ AKGR++AE+ M Sbjct: 300 GTMGGGISMNFLSAGIPVTIAEMQQEALDRGTGTIRKNYEATAAKGRMTAEQVEGAMGLL 359 Query: 369 SGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVS 428 + + LA DL+IEAV+E++ VK+ +F +LD++ K GA+LA+NTSYL ID +AS+ Sbjct: 360 KSTLDLNDLAECDLIIEAVYENMDVKKDIFGKLDKIAKPGAILASNTSYLSIDEIASATG 419 Query: 429 RPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNR 488 RP DV+G+HFFSPANIMKLLEVV + DV+AT +LAKK++K V AGVC GFIGNR Sbjct: 420 RPGDVVGMHFFSPANIMKLLEVVRGAKTDKDVLATVMDLAKKIKKVAVVAGVCYGFIGNR 479 Query: 489 VLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNP 548 +L + A ++ +GA+P Q+D FG PMGPFQ+ DLAG DIGW R+P Sbjct: 480 MLIPRQMEAMKLLHEGATPMQVDKVHVEFGMPMGPFQMSDLAGVDIGW--------HRDP 531 Query: 549 AARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFT 608 R I D L +GQK+ GFY Y + R+ +P P V II+ R + G T Sbjct: 532 -TRIENIRDALAAENRWGQKTKAGFYDY-DDKRNPSPSPRVAEIIEEFRTKTGTPQHEVT 589 Query: 609 DEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKI 668 DEEI+ R M+NEGA ++ E +A R D+DV ++YGYG+P YRGGPM +AD VGL I Sbjct: 590 DEEIMERTFYTMVNEGAKILEEGMAQRASDIDVVWIYGYGWPPYRGGPMFWADQVGLKTI 649 Query: 669 LADIREFAKEDPLFWKPSPLLIELVERGADF 699 +A + + ++ S LL + E G F Sbjct: 650 VAGLEKHG------FEISKLLRDKAESGGKF 674 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: 1110 Number of extensions: 44 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: 676 Length adjustment: 39 Effective length of query: 667 Effective length of database: 637 Effective search space: 424879 Effective search space used: 424879 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