Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF1550 HP15_1512 multifunctional fatty acid oxidation complex subunit alpha
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Marino:GFF1550 Length = 715 Score = 335 bits (858), Expect = 6e-96 Identities = 226/677 (33%), Positives = 349/677 (51%), Gaps = 35/677 (5%) Query: 39 NAAVADPAVQAIVLVCAGRTFIAGADITEF-----GKPPQPPA----LNDVIAALENSPK 89 +A A ++ +V+ + +FI GADITEF G A N+V A+E+ P Sbjct: 45 DALKAQKNLKGLVVTSSKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPF 104 Query: 90 PTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELA 149 PT+ AI+G ALGGG E+ L +RV K+AK+GLPEVKLG+ PG GGT RL R VG + A Sbjct: 105 PTVTAINGMALGGGFEMCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNA 164 Query: 150 VQMIVGGSPIGAAEALKHGLVEEVVEN--LVAGAVAFAKKVLAEKRPLRRLRDDDS---K 204 V+ I GG+ A ALK G V+ V+++ LV AVA + K R++ K Sbjct: 165 VEWISGGTENRADVALKVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIK 224 Query: 205 LAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVS 264 L A ++ + + K + AP + + ++ ++ E +GF K+ + Sbjct: 225 LNAMESMMAFEISKAFVAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKT 284 Query: 265 DQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLI 324 + + F ++E K + + V+ A++GAG MGGG+A A G P+ + Sbjct: 285 NVAACLVGLFLNDQELKKKAKAWE-KEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMK 343 Query: 325 ETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFE 384 + ++ + GL +K +G + PD A + IT + + K+ DL++EAV E Sbjct: 344 DINQDGIALGLKEAKKLLSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVE 403 Query: 385 TMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCE 444 VK V + + +L SNTS +SID +A KRP++ GMHFF+P ++M L E Sbjct: 404 NPKVKDAVLRETEDAVREDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVE 463 Query: 445 IVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQ 504 ++RG KT+ A+ T V+ AK + K P+VV C GF+ NR+L L+ +GA Q Sbjct: 464 VIRGEKTSDRAIATTVAYAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQH 523 Query: 505 VDAVVTKFGMPMGPFAMGDLAGLDIGWRSRK-------DRGIKSE---IADALCEAGRFG 554 VD V+ KFG PMGP + D+ G+D G + + DR +K E D + + R+G Sbjct: 524 VDKVMEKFGWPMGPAYLLDVVGMDTGKHAGEVMADGFPDR-MKHEGTTAIDVMFDNNRYG 582 Query: 555 QKTGKGYYKYE---QGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINE 611 QK KG+YKYE +G + + D E L+ + + + ++E+I+ RM+ P+ E Sbjct: 583 QKNDKGFYKYELDRKGKQKKVVDEETYKLLEPVVQ----GKNEFSEEDIIARMMIPLCLE 638 Query: 612 GARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPS 671 R LE+ I P+D D+ ++G G+P +RGG + Y D +G+ E +A P Sbjct: 639 TVRCLEDGIVEDPADADMGLIFGIGFPPFRGGALRYIDDMGVDKFVELADKFADL--GPL 696 Query: 672 LEPAPLLARLAAEGKTF 688 P L +A GK F Sbjct: 697 YHPTEKLREMAKTGKKF 713 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: 1034 Number of extensions: 60 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: 699 Length of database: 715 Length adjustment: 39 Effective length of query: 660 Effective length of database: 676 Effective search space: 446160 Effective search space used: 446160 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: 55 (25.8 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