Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__PV4:5209977 Length = 706 Score = 370 bits (951), Expect = e-106 Identities = 251/700 (35%), Positives = 363/700 (51%), Gaps = 33/700 (4%) Query: 13 VAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGR-TFIAGADITEFG 69 +A++T+D P +N L A I E + AD ++ +V++ + +F+AGADI+ Sbjct: 14 IAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADISMLD 73 Query: 70 KPPQPPAL-------NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK-- 120 ++V ALE+ P +AAI+G LGGGLE+AL CH RV K Sbjct: 74 ACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSNKTM 133 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAG 180 LGLPEV+LGLLPG GGTQRLPR VG ++ M++ G + A +ALK GLV++VV + Sbjct: 134 LGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVVPESILL 193 Query: 181 AVAFAKKVLAEKRPLRR--LRDDDSKLAAAKADRSI-FTNAVAAMTKKARG-LEAPFACA 236 A + LA RP ++ L + L R+I F A+ + KK +G AP Sbjct: 194 QTAI-EMALAGARPAKKPKLSTVEKLLEGTPVGRNIIFEQALKQVNKKTQGNYPAPEKII 252 Query: 237 DAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVS 296 D + + +GL+ E + F LVVS++S+A R FFA E K G D P+ V+ Sbjct: 253 DCVRQGVTKGIVKGLEVEAQHFGDLVVSNESEALRSIFFATTEMKKESGAGD-VSPKAVN 311 Query: 297 RVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDA 355 +V ++G G MGGGIA ++ A IPV + + E L L K R + P Sbjct: 312 KVMVLGGGLMGGGIASVTTTKAKIPVRVKDISEIGLSNALAYAYKLLAKGVKRRHMTPAV 371 Query: 356 PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSI 415 MAL+T + +KDAD+++EAVFE + +K ++ V+ + ASNTS L I Sbjct: 372 RDNLMALMTTTTEYKGIKDADMVVEAVFEDLNLKHQMVKDVERECGEHTIFASNTSSLPI 431 Query: 416 DEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGV 475 +IA +RP++V+G+H+FSP M L E++ KT+P + T V+ A+K K P+VV Sbjct: 432 KQIAEAAERPENVIGLHYFSPVEKMPLVEVIAHDKTSPQTIATTVAFARKQGKTPIVVKD 491 Query: 476 CDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWR--- 532 GF NR+LA ++ LL EG +D + KFG P+GP + D G+D+G + Sbjct: 492 GAGFYVNRILALYMNEAANLLLEGQSVDHLDKALVKFGFPVGPMTLLDEVGIDVGAKISP 551 Query: 533 -SRKDRG--IKSEIA-DALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKL 588 K+ G K+ A D L R G+K GKG+Y+Y S+ + D V ++ T Sbjct: 552 ILEKELGERFKAPAAFDKLLADDRKGRKNGKGFYQYGAKSKKKLVDESVYGVLGLT---- 607 Query: 589 GLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYA 648 D + ER V M+NE R LEE I A P D D+ ++G G+P + GGP Y Sbjct: 608 --PGADGEPIALAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPPFLGGPFRYM 665 Query: 649 DSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 DS+G KH+ E L Y D P L +A G F Sbjct: 666 DSLGAKHLVETLKRYQDQFGD-RFAPCDRLVEMAESGSKF 704 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: 1047 Number of extensions: 55 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: 706 Length adjustment: 39 Effective length of query: 660 Effective length of database: 667 Effective search space: 440220 Effective search space used: 440220 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