Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate AO353_05300 AO353_05300 aldehyde dehydrogenase
Query= metacyc::MONOMER-15203 (503 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05300 Length = 481 Score = 276 bits (706), Expect = 1e-78 Identities = 170/481 (35%), Positives = 256/481 (53%), Gaps = 9/481 (1%) Query: 3 IKRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDT 62 +KR +++I G G A+ + V G+ A A A V++A+ AA+AAFPAWS + Sbjct: 4 VKRFDNFIGGQWVAG-AEYSININPSELSDVIGEYAKADLAQVNAAIDAARAAFPAWSTS 62 Query: 63 PPIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLK 122 R+ + K + A ++EL + RE GK +A GEV+R +I +F G L Sbjct: 63 GIQARSDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVSRAGNIFKFFAGECLRLS 122 Query: 123 GDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPS 182 GDY V G++ TR+ LGVV ITP+NFP+ +P W A+A GN VLKP+ L P Sbjct: 123 GDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPAELVPG 182 Query: 183 ASLMMADLLKQAGLPDGVFNVVQGDKDSV-EALIDHPDVKALSFVGSTPIANLIYERGAR 241 + +A+++ +AG P GVFN+V G + +A+++ P V +SF GS + I Sbjct: 183 CAWALAEIISRAGFPAGVFNLVMGSGRVIGDAMVNSPKVDGISFTGSVGVGRQIAVNCVS 242 Query: 242 SGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVP 301 ++Q G KN +++ DA+L +AV+ + +A+ S G+RC A S ++ + DK V Sbjct: 243 RQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDKFVE 302 Query: 302 RLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTG 361 +AER + +K+ + L+ ++GP+V+ ++ YI+ G +EGA +V G VT Sbjct: 303 AMAERMKSIKVGHALKSGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGG----GLVTC 358 Query: 362 EGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCF 421 + +G+++ TLF M I REEIFGPV VRV D A+ + ND EFG Sbjct: 359 D--TEGYYLAPTLFADSEAAMRISREEIFGPVANIVRVADYDAALAMANDTEFGLSAGIA 416 Query: 422 TESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQK 481 T S A F R Q GMV +N+P FGG K S +G + G FYT K Sbjct: 417 TTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG-SREQGRYAQEFYTVVK 475 Query: 482 S 482 + Sbjct: 476 T 476 Lambda K H 0.319 0.136 0.406 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: 559 Number of extensions: 24 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: 503 Length of database: 481 Length adjustment: 34 Effective length of query: 469 Effective length of database: 447 Effective search space: 209643 Effective search space used: 209643 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