Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF1257 HP15_1232 fatty acid oxidation complex subunit alpha
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Marino:GFF1257 Length = 716 Score = 303 bits (776), Expect = 2e-86 Identities = 219/725 (30%), Positives = 344/725 (47%), Gaps = 45/725 (6%) Query: 1 MSEVVTRATQDQVAIVTVDSP--PVNALSAAVRRGILENVNAAVAD-PAVQAIVLVCAGR 57 MS + DQ+ +T+D P N ++AA R + E D ++ I++ A + Sbjct: 1 MSAIRYELGSDQILTLTIDMPGQSANTMNAAFRDALSETAAKVKEDLDNIRGIIIASAKK 60 Query: 58 TFIAGADITEFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVAL 108 TF AG D+ E K + A L + LE + KP +AAI+G+ALGGGLE+AL Sbjct: 61 TFFAGGDLKELHKVTREDARTFEDMVNGLKSHMRFLETTGKPVVAAINGSALGGGLEIAL 120 Query: 109 GCHFRVAVKE--AKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALK 166 CH+RVA+ + +LGLPEV LGLLPG GGTQRLPR +G E A ++ G + ALK Sbjct: 121 ACHYRVAINDDSIQLGLPEVTLGLLPGGGGTQRLPRMIGLEAAFPFLMEGKKVNPKAALK 180 Query: 167 HGLVEEVVENLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAA------KADRSIFTNAVA 220 G++ E+ ++ A + + E P + D A A A Sbjct: 181 AGIINELADS--ADDMITKARAFIEANPKCQQPWDQKGFRFPGGAPHHPAMAQKLAIAPA 238 Query: 221 AMTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAERE 279 + +K +G AP A + F+ G E F +LV+ +K F+ + Sbjct: 239 MLKQKTKGCYPAPERILSAAVEGAQVDFDNGSLIETRYFAELVIGQVAKNMTGTFWFQLN 298 Query: 280 AAKVDGV-PDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIM 338 A K G P+G + +V ++GAG MG GIA S A GI V L + E ++G Sbjct: 299 AIKAGGSRPEGVEKETFRKVGVLGAGMMGAGIAYSTATRGIDVVLKDVSVENAEKGKSYS 358 Query: 339 QKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDA 398 + +RG + + A ++ I ++++ DL+IEAVFE +K +V + Sbjct: 359 ENLLAKKVSRGRMTEEQKADILSRIKATDSSDDLEGCDLVIEAVFEDSGLKAKVTQEAEP 418 Query: 399 HAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLT 458 + ASNTS + I ++A + ++ +G+HFFSP + M+L EI+ G KT+ + L Sbjct: 419 KLVANGIFASNTSTIPITQLAGASANAENFIGLHFFSPVDKMQLVEIIVGEKTSDETLAR 478 Query: 459 AVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGP 518 + ++I K+PVVV GF +R+ + +L EG P ++ GMP+GP Sbjct: 479 SFDYVQQIGKIPVVVNDSRGFFTSRVFGTFVNEGICMLGEGIHPASIENAGVLAGMPVGP 538 Query: 519 FAMGDLAGL----DIGWRSRKDRGI---------KSEIADALC-EAGRFGQKTGKGYYKY 564 A+ D + I +SRKD + DA+ E GR G+ G G+Y+Y Sbjct: 539 LAISDEVSMTLMQHIRDQSRKDTEAAGGTWNPHPAEAVIDAMVNEHGRKGKAAGAGFYEY 598 Query: 565 EQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARP 624 + + PE+ETL + K R + +E+ +R+++ E R LEE + Sbjct: 599 PANGKKHL-WPELETLFVN-----AEKARTVKLQELKDRILFIQAIETVRCLEEGVLRTV 652 Query: 625 SDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAE 684 D ++ ++G G+ + GG + + + G++ ER SA A+ T P LL A Sbjct: 653 EDANIGSIFGIGYAPWTGGAIQFINQYGVRAFTERASALAE-TYGERFAPPKLLQEKAET 711 Query: 685 GKTFA 689 FA Sbjct: 712 NTPFA 716 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: 1040 Number of extensions: 52 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 699 Length of database: 716 Length adjustment: 39 Effective length of query: 660 Effective length of database: 677 Effective search space: 446820 Effective search space used: 446820 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