Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC
Query= metacyc::MONOMER-15203 (503 letters) >FitnessBrowser__Phaeo:GFF3171 Length = 503 Score = 233 bits (595), Expect = 9e-66 Identities = 157/484 (32%), Positives = 247/484 (51%), Gaps = 24/484 (4%) Query: 6 IEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPI 65 I + I G G A Q ++ P V VA + AD+D+A AA+ AF W D P + Sbjct: 23 IRNRIAGADVAGGAGVFQTIS-PVDKSVICDVAHGTAADIDAAAQAARQAFAEWRDLPAV 81 Query: 66 RRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVE-FACGIPQLLKGD 124 +R +++ + E + A +E+A + G+ + RG + FA + Q G Sbjct: 82 QRKKILIRIAEGIEARAEEIALCECWDTGQAYKFMSKAALRGAENFRYFADQVVQARDGQ 141 Query: 125 YTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSAS 184 + + S + N TTR P+G V ITP+N P M+ W A+AAG + V KP+ P + Sbjct: 142 HLQ--SPTLMNVTTRVPIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTA 199 Query: 185 LMMADLLKQAGLPDGVFNVVQGDKDSV-EALIDHPDVKALSFVGSTPIANLIYERGARSG 243 ++ ++ ++AGLP GV N V G D +AL +HP ++A++FVG + +LI ++GA + Sbjct: 200 RLLVEIAEEAGLPPGVLNTVNGFGDEAGKALCEHPAIRAIAFVGESRTGSLITKQGADTL 259 Query: 244 KRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRL 303 KR G KN ++V DA+L++A+DA+I Y GERC + S ++ + D RL Sbjct: 260 KRNHLELGGKNPVIVFEDADLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARL 319 Query: 304 AERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEG 363 ER ++K+ + L+ E+GP+V+ + ++T Y + EGA + G GE Sbjct: 320 IERINNIKVGHPLDPTTEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGEP-----VGE- 373 Query: 364 CADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTE 423 +G+++ TLF +M I +EEIFGPVL + A A+ L ND +G +T Sbjct: 374 --EGYFIRPTLFTDARNDMRIAQEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTN 431 Query: 424 SGSVAREFGRRIQVGMVGINVP----IPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTK 479 + A F R++ GM+ +N +P P FGG K S G G+ FY + Sbjct: 432 DLTRALRFTDRLEAGMIWVNSENVRHLPTP-----FGGVKASGIG--RDGGDWSFEFYME 484 Query: 480 QKSI 483 QK I Sbjct: 485 QKHI 488 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: 562 Number of extensions: 24 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: 503 Length of database: 503 Length adjustment: 34 Effective length of query: 469 Effective length of database: 469 Effective search space: 219961 Effective search space used: 219961 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