Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__SB2B:6938034 Length = 706 Score = 373 bits (957), Expect = e-107 Identities = 253/703 (35%), Positives = 367/703 (52%), Gaps = 34/703 (4%) Query: 11 DQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCA-GRTFIAGADITE 67 D +A++T+D P +N L A I + AD +++ +VL+ +F+AGADI+ Sbjct: 12 DGIALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKADSFVAGADISM 71 Query: 68 FG--KPPQPPAL-----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 + + L + V A LE P +AAIHG LGGGLE+AL CH RV +K Sbjct: 72 LDACETAEDARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALACHQRVCSDSSK 131 Query: 121 --LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLV 178 LG+PEV+LGLLPG GGTQRLPR +G A+ +++ G + +A+K GLV++VV + Sbjct: 132 TMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKMGLVDDVVPESI 191 Query: 179 AGAVAFAKKVLAEKRPLRRLRDD--DSKLAAAKADRSI-FTNAVAAMTKKARG-LEAPFA 234 A + LA K+ + L+ L R+I F A + KK +G +P Sbjct: 192 LLDTAI-EMALAGKKTRKPLKQPLVTKLLEGTPVGRNIMFDQATKQVLKKTQGNYPSPLK 250 Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294 D + + E+GL+ E F LV + +S A R FFA E K G D KPR Sbjct: 251 IIDCVREGMAKGMEKGLEVEAAHFGALVATPESAALRSIFFATTEMKKETGAGDA-KPRK 309 Query: 295 VSRVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPP 353 V++ ++G G MGGGIA ++ A +PV + + ++ L LG K + R + Sbjct: 310 VAKAVVLGGGLMGGGIASVTTTKAKVPVRVKDISDKGLSNALGYAYKLLDKGVKRRHMTS 369 Query: 354 DAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYL 413 K MAL+T VKDAD+++EAVFE + +K ++ ++ + ASNTS L Sbjct: 370 AERDKLMALMTTTTEYRGVKDADIVVEAVFEDLNLKHQMVRDIERECGEHTIFASNTSSL 429 Query: 414 SIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVV 473 I +IAA RP++V+G+H+FSP M L E++ KT+P+ + T V+ A+K K P+VV Sbjct: 430 PITQIAAAASRPENVIGLHYFSPVEKMPLVEVIAHEKTSPETIATTVAFARKQGKTPIVV 489 Query: 474 GVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWR- 532 C GF NR+LA ++ +LL EG +D + KFG P+GP + D G+D+G + Sbjct: 490 KDCAGFYVNRILALYMNEAAQLLLEGQAVDHLDKALVKFGFPVGPMTLLDEVGIDVGAKI 549 Query: 533 ---SRKDRG--IKSEIA-DALCEAGRFGQKTGKGYYKY-EQGSRAPMPDPEVETLINDTL 585 K+ G K+ A D L R G+K GKG+Y Y + + D V +L+ T Sbjct: 550 SPILEKELGERFKAPAAFDKLMADDRKGRKNGKGFYLYGKAAKKGKKVDESVYSLLGLTP 609 Query: 586 AKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPM 645 A EI ER V M+NE R LEE I A P D D+ ++G G+P + GGP Sbjct: 610 A------TGKEAGEIAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPPFLGGPF 663 Query: 646 HYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 Y D++G + L Y D PA LL +AAEGKTF Sbjct: 664 RYMDTLGAAKMVRLLEGYQSKYGD-RFAPAALLKAMAAEGKTF 705 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: 1038 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: 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