Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 7024269 Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__ANA3:7024269 Length = 709 Score = 378 bits (971), Expect = e-109 Identities = 254/703 (36%), Positives = 368/703 (52%), Gaps = 29/703 (4%) Query: 10 QDQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGR-TFIAGADIT 66 +D +AI+ +D P +N L A I E ++ D +++ +VL+ + +F+AGADI+ Sbjct: 11 EDGIAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKKDSFVAGADIS 70 Query: 67 EFGK---PPQPPALND----VIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119 AL+ V LE P +AAIHG LGGGLE+AL CH RV + Sbjct: 71 MLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALACHQRVCSDDG 130 Query: 120 K--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN- 176 K LG+PEV+LGLLPG GGTQRLPR VG A+ M++ G I +ALK GLV +VV Sbjct: 131 KTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKMGLVNDVVPQT 190 Query: 177 -LVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARG-LEAPFA 234 L+ AV A +P+++ + IF A + KK +G AP Sbjct: 191 ILLQTAVEMALAGKRTAKPVKKSLVNQLLEGTGFGRNIIFDQAAKQVVKKTQGNYPAPAK 250 Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294 D + + ++GL+ E F +LVVS +S+A R FFA E K G +G PR Sbjct: 251 IIDCVRQGMAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTEMKKETGA-EGATPRK 309 Query: 295 VSRVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPP 353 V + I+G G MGGGIA ++ A IP + + E+ L L K + R + P Sbjct: 310 VKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAYKLLDKGVKRRHMTP 369 Query: 354 DAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYL 413 MAL+T + VKDAD+++EAVFE +A+K ++ ++ + ASNTS L Sbjct: 370 AVRDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERECGEHTIFASNTSSL 429 Query: 414 SIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVV 473 I +IA RP++V+G+H+FSP M L E++ AKT+P+ + T V+ A+K K P+VV Sbjct: 430 PIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATTVAFARKQGKTPIVV 489 Query: 474 GVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWR- 532 GF NR+LA ++ +LL EG + +D + KFG P+GP + D G+D+G + Sbjct: 490 QDGAGFYVNRILALYMNEAAQLLLEGQSIEHLDKALVKFGFPVGPITLLDEVGIDVGAKI 549 Query: 533 ---SRKDRG--IKSEIA-DALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLA 586 K+ G K+ A D L R G+K GKG+Y+Y G++A V+ A Sbjct: 550 APILEKELGERFKAPAAFDKLLSDDRKGRKNGKGFYQYAAGNKASSKKKAVD---ESVYA 606 Query: 587 KLGLK-RRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPM 645 LG+K D + ER V M+NE R L++ I A P D D+ ++G G+P + GGP Sbjct: 607 VLGIKPGMDKDLSAVAERCVVQMLNEAVRCLDDGIIASPRDGDIGAIFGIGFPPFLGGPF 666 Query: 646 HYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 HY D++G ++ L Y D EP P L +AAE F Sbjct: 667 HYIDTLGADNLVNILERYQAQYGD-RFEPCPRLKAMAAEKARF 708 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: 998 Number of extensions: 52 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: 709 Length adjustment: 39 Effective length of query: 660 Effective length of database: 670 Effective search space: 442200 Effective search space used: 442200 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