Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate RR42_RS10265 RR42_RS10265 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Cup4G11:RR42_RS10265 Length = 692 Score = 583 bits (1504), Expect = e-171 Identities = 311/685 (45%), Positives = 430/685 (62%), Gaps = 8/685 (1%) Query: 18 VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77 V +++I + PVN L DVR G++ I+ A AD V A+++ GAG+ F GAD+REF P Sbjct: 11 VAVISIANPPVNGLGYDVRVGIIDGIDRAAADDNVRAIVLTGAGKAFSGGADMREFNSPE 70 Query: 78 V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135 P L V IE K VVAA+H A+GGGLE+ALA HYR+AV A++ L EV +GL Sbjct: 71 AWREPGLNTVLVAIENSIKLVVAAVHSVAMGGGLELALACHYRVAVPKARIALSEVTMGL 130 Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHEL 195 LPGAGGTQR PRLIG +AA ++I+ G ++ GL DRL D + A +A+ E+ Sbjct: 131 LPGAGGTQRLPRLIGLEAATNMIVHGTSIPSEALADTGLFDRLVEGDVVTA-AVAFAQEV 189 Query: 196 LAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDE 255 A P R RD AVA R A + + L +PL+ +DA+EA+ + PFDE Sbjct: 190 AARPGPHPRVRDLTIRHPTPEGYLAVA--RPAVAARYKNLQAPLRCLDAIEASFKLPFDE 247 Query: 256 GLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVGGGTMGAG 314 GL +ER+LFLE ++ P L HAFF+ER K + + P R +N + VVG G MG+G Sbjct: 248 GLALERRLFLELMNGPVSKSLRHAFFSERAAAKLADVPDSVPERAVNKVAVVGAGLMGSG 307 Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374 IA+ L AG+PV +++ D + +G A I + Y+ + KG+L AE A M+ + Sbjct: 308 IAMNFLSAGIPVVLLDISDEVVQKGAAAIRRNYEASLKKGKLRAEVVEARMALLQPTVDL 367 Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434 +A DLVIEA++ED+ VK +F LD + + GA+LATNTS LD+D +A+ RP DV+ Sbjct: 368 GRVAACDLVIEAIYEDMDVKLRMFRALDEIARPGAILATNTSMLDVDRIAAETRRPQDVV 427 Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494 GLHFFSPAN+M+LLEVV + + DV+ TA LA+++ K PV +GVCDGFIGNR+LA Y Sbjct: 428 GLHFFSPANVMRLLEVVRGAKTAPDVLQTAMRLARRIGKVPVVSGVCDGFIGNRMLAKYT 487 Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554 A ++E GA P Q+D A+ FG MGPF++ DLAG DIGWA RKR A +P+ + Sbjct: 488 RRAGELLEQGAFPEQVDRAIEEFGLAMGPFRMADLAGNDIGWAIRKRHYA-EDPSQPRFE 546 Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIR 614 + DRLCE G FGQK+G G+Y Y G R P A+++A G+ PR F+ +EI+ Sbjct: 547 LGDRLCEAGHFGQKTGTGWYDYEAGQRKALPSARTRAMLEAYWKERGVVPRRFSGQEIVE 606 Query: 615 RYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIRE 674 R + A++NEGA V+ E IA R D+D +L+GYGFP +RGGPM YAD VG+ + +R Sbjct: 607 RLIYALVNEGAAVLDEGIAARASDIDAVYLHGYGFPAWRGGPMFYADTVGVTNVRRTLRA 666 Query: 675 FAKEDPLFWKPSPLLIELVERGADF 699 + +DP WKP+ L+ +L ++G F Sbjct: 667 LSAKDP-SWKPAALIEQLADKGRTF 690 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: 1063 Number of extensions: 49 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: 692 Length adjustment: 39 Effective length of query: 667 Effective length of database: 653 Effective search space: 435551 Effective search space used: 435551 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