Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 275 bits (702), Expect = 3e-78 Identities = 161/476 (33%), Positives = 255/476 (53%), Gaps = 7/476 (1%) Query: 6 KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65 K ++INGE+VE V+ AT E + V +T ++ A TA A K W+++ Sbjct: 8 KASHFINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTG 67 Query: 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMG 124 R RIL ++ + +L+ L T + GK +E L + G + +E+ G + + G Sbjct: 68 TERGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTG 127 Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184 + + V R +G+ GI +N+P + CW A+A GN+ + KPSE TPL Sbjct: 128 EHIPLGEDWVYTK--REALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLC 185 Query: 185 TEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENL 244 K+ E+ +AG P GVFNVV G +V ++ P + +S GS P G+ VY +E + Sbjct: 186 ALKVAEILIEAGAPAGVFNVVQGMGEVGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEGM 245 Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304 K V G K+ I+ +DA++++ V + F S+G+ C V V++GI ++F+A+L Sbjct: 246 KHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARL 305 Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364 E+ + +G+ +D+ GP++ E+ L YIEKG EEGARL+C GR DGYF+ Sbjct: 306 AERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGR-RADMDGYFI 364 Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424 PT+F +VT +MTI ++EIF PV+SV+ +E + AN +EF A +FT + Sbjct: 365 EPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHR 424 Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480 N++AG IN AP+ PF G K+S G N K+++ +++ K V R Sbjct: 425 VIGNLEAGSCFINSYNDAPVE-APFGGVKAS--GVGRENSKEAIKHFSQVKSVYVR 477 Lambda K H 0.318 0.136 0.396 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: 600 Number of extensions: 36 Number of successful extensions: 3 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: 487 Length of database: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 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: 52 (24.6 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