Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 202205 SO3088 fatty oxidation complex, alpha subunit (NCBI ptt file)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__MR1:202205 Length = 707 Score = 375 bits (963), Expect = e-108 Identities = 256/704 (36%), Positives = 370/704 (52%), Gaps = 35/704 (4%) Query: 10 QDQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGR-TFIAGADIT 66 +D +AI+T+D P +N L A I E ++ D +++ +VL+ + +F+AGADI+ Sbjct: 13 EDGIAILTMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKKDSFVAGADIS 72 Query: 67 EFGK---PPQPPALND----VIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119 AL+ V LE P +AAIHG LGGGLE+AL CH RV + Sbjct: 73 MLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALACHQRVCSDDG 132 Query: 120 K--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENL 177 K LG+PEV+LGLLPG GGTQRLPR VG A+ M++ G I +ALK GLV +VV Sbjct: 133 KTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKMGLVNDVVPQT 192 Query: 178 V----AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARG-LEAP 232 + A +A A K +A +P+++ + IF A + KK +G AP Sbjct: 193 ILLQTAVEMALAGKQIA--KPVKKSLVNQLLEGTGFGRNIIFDQAAKQVAKKTQGNYPAP 250 Query: 233 FACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKP 292 D + I ++GL+ E F +LVVS +S+A R FFA E K G +G P Sbjct: 251 AKIIDCVRQGIAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTEMKKETGA-EGATP 309 Query: 293 RPVSRVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGL 351 R V + I+G G MGGGIA ++ A IP + + E+ L L K + R + Sbjct: 310 RKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAYKLLDKGVKRRHM 369 Query: 352 PPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTS 411 P A MAL+T + VKDAD+++EAVFE +A+K ++ ++ + ASNTS Sbjct: 370 TPAARDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERECGEHTIFASNTS 429 Query: 412 YLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPV 471 L I +IA RP++V+G+H+FSP M L E++ AKT+P+ + T V+ A+K K P+ Sbjct: 430 SLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATTVAFARKQGKTPI 489 Query: 472 VVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGW 531 VV GF NR+LA ++ +LL EG + +D + KFG P+GP + D G+D+G Sbjct: 490 VVQDGAGFYVNRILALYMNEAAQLLLEGQSVEHLDKALVKFGFPVGPITLLDEVGIDVGA 549 Query: 532 R----SRKDRG--IKSEIA-DALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDT 584 + K+ G K+ A D L R G+K GKG+Y+Y S+ D ET+ Sbjct: 550 KISPILEKELGERFKAPAAFDKLLSDDRKGRKNGKGFYQYGAASKKKAVD---ETVYGVL 606 Query: 585 LAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGP 644 K G+ D + ER V M+NE R L+ I A P D D+ ++G G+P + GGP Sbjct: 607 GIKPGV---DKEMSAVAERCVVQMLNEAVRCLDAGIIASPRDGDIGAIFGIGFPPFLGGP 663 Query: 645 MHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 HY D++G ++ + L Y D EP L +AAE F Sbjct: 664 FHYIDTLGADNLVKILERYQTQYGD-RFEPCQRLKAMAAEKARF 706 Lambda K H 0.317 0.134 0.383 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: 1013 Number of extensions: 56 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: 699 Length of database: 707 Length adjustment: 39 Effective length of query: 660 Effective length of database: 668 Effective search space: 440880 Effective search space used: 440880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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