Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 233 bits (594), Expect = 1e-65 Identities = 152/456 (33%), Positives = 230/456 (50%), Gaps = 9/456 (1%) Query: 25 NVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRRSRVMFKFKELLDRHHD 84 +V NPA G + A VA + A+ +A A PAW+ +++ R ++ ++ +L+ H D Sbjct: 28 DVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAARTAKERGAILRRWSDLILAHAD 87 Query: 85 ELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDNIGGGIDNWNLRQPLG 144 +LA++++ E GK L++A GEV G +++ G +++QP+G Sbjct: 88 DLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYGHTIPTPMPGKRLASIKQPVG 147 Query: 145 VCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMARLLTEAGLPDGVFNV 204 VCA + P+NFP+ + + AL AG ++KP+ P ++L +ARL TEAG+P GV N+ Sbjct: 148 VCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLSALAIARLATEAGVPAGVLNI 207 Query: 205 VQGDKVAV--DALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKRVQALGGAKNHMIVMPD 262 V + + L + +SF GSTPI + ++QQ K++ G IV D Sbjct: 208 VTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAGTMKKLSLELGGNAPFIVFDD 267 Query: 263 ADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRIDQLKIGNGQQPGTD 322 ADL+ A D I + Y +AG+ C+ + + + D A+L ++ LK+G G G Sbjct: 268 ADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFAARLAEKVAALKVGPGTGEGVQ 327 Query: 323 MGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFVGATLFDQVTAEMSIY 382 +GPL+ + KV G + V GA ++ G V G G F T+ T EM I+ Sbjct: 328 IGPLINEKALTKVVGLVSGAVQAGAEVLTGG---DVHGL-GGHFYQPTVLVGATPEMRIF 383 Query: 383 QQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAFARSIKVGMVGINVP 442 Q+EIFGPV IV+ A AV L NA FG ++RD G A I+ GMVGIN Sbjct: 384 QEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRCWRVAEQIEAGMVGINEG 443 Query: 443 IPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYK 478 + + FGG K S G A EGL Y K Sbjct: 444 L-ISTEVAPFGGVKESGLGREGA--SEGLDEYLETK 476 Lambda K H 0.320 0.137 0.412 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: 551 Number of extensions: 20 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: 500 Length of database: 485 Length adjustment: 34 Effective length of query: 466 Effective length of database: 451 Effective search space: 210166 Effective search space used: 210166 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