Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= reanno::WCS417:GFF2142 (499 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 231 bits (588), Expect = 5e-65 Identities = 152/460 (33%), Positives = 234/460 (50%), Gaps = 19/460 (4%) Query: 23 VFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRARVLFEYLHLLRERKDD 82 V +PATG LAS + AVAAA+ AF GWA TP RA + + KD+ Sbjct: 21 VIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAILAIADSIEAAKDE 80 Query: 83 LARIIVAEHGKVFTDAQGEVDRGIDILEFACGIP---NLLKGEHSDQVSRGMDNWTMRQP 139 LAR++ AE GK +A GE+ + G+ ++LK + S +V R+P Sbjct: 81 LARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVLKDDDSVRVE------VHRKP 134 Query: 140 LGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASLFMAELLREAGLPKGVF 199 LGVVA ++P+NFPVM+ +W + AGNT ++KPS P A+L M E+ A LP GV Sbjct: 135 LGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIAN-AHLPPGVL 193 Query: 200 NVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYIYETGARNGKRVQGLGGAKNHMVVMPD 259 N V G+ E A+ HP + + F GSTP + I GA N KR+ G + +V+PD Sbjct: 194 NSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLELGGNDAAIVLPD 253 Query: 260 ADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALTERAKHLRITDGRDLKAE 319 AD++K + A+G++G+ C A+ + + D + L E A+ + G D ++ Sbjct: 254 ADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVGPGSDAASQ 313 Query: 320 MGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPGLENGFWLGATLFDHVTEEMS 379 GP+ +R + + + G + L G E +G++ ++ VT+ M Sbjct: 314 FGPVQNRKQFDLVRALADDARAHGGRFLAGG------EAREGDGYFFPLSVVVDVTDGMR 367 Query: 380 IYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDGNIAREFARRIEVGMVGIN 439 I EE FGP+L +R +D +A+ NA+E G G S ++ D A FA+R+E G V +N Sbjct: 368 IVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWVN 427 Query: 440 VPISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFYTKQKSI 479 S+ FGG K+S G +G G+ Y + +++ Sbjct: 428 DHASISPD-VPFGGAKQSGVGT--EFGLYGLEEYMQLQTV 464 Lambda K H 0.320 0.136 0.407 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: 541 Number of extensions: 28 Number of successful extensions: 4 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: 499 Length of database: 469 Length adjustment: 34 Effective length of query: 465 Effective length of database: 435 Effective search space: 202275 Effective search space used: 202275 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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