Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= metacyc::MONOMER-15203 (503 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 265 bits (677), Expect = 3e-75 Identities = 170/475 (35%), Positives = 242/475 (50%), Gaps = 8/475 (1%) Query: 10 INGHKTNGVADSHQEVTNPA-TGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRA 68 I G T+GV TNP+ T V G A+AS+ AVAAA AAFPAWS + P +R Sbjct: 39 IGGAWTDGVRTYQN--TNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRF 96 Query: 69 RVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQ 128 ++ + A K EL + + RE GK +A GEV R I +F G G+ Sbjct: 97 DILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGGEVMPS 156 Query: 129 VSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMA 188 V G+ TR+PLG + ITP+NFP+ +P W A+A GN V KP+ + P ++ +A Sbjct: 157 VRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWALA 216 Query: 189 DLLKQAGLPDGVFNVVQGDKDSVEA-LIDHPDVKALSFVGSTPIANLIYERGARSGKRIQ 247 D+L +AGLP GVFN+V G V A L++ + +SF GS + G ++Q Sbjct: 217 DILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPRGAKVQ 276 Query: 248 ALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERA 307 G KN VV+ DA+L+ AV A I + + S G+RC A S ++ + D+ V + E+ Sbjct: 277 LEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAAMVEKM 336 Query: 308 RDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADG 367 + LK+ + + ++GP+V + + YI G EGA++ G + + G A G Sbjct: 337 KTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADG---APG 393 Query: 368 FWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSV 427 F++ LF TP M I REEIFGPV++ +R + A+ L ND FG T S Sbjct: 394 FYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTSLKH 453 Query: 428 AREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKS 482 A F R Q GMV +N+P FGG K S +G G FYT K+ Sbjct: 454 ATHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKSSSYG-PREQGRYAAEFYTTVKT 507 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: 645 Number of extensions: 33 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: 512 Length adjustment: 34 Effective length of query: 469 Effective length of database: 478 Effective search space: 224182 Effective search space used: 224182 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