Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate PfGW456L13_1795 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= reanno::Koxy:BWI76_RS03070 (501 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1795 Length = 482 Score = 235 bits (600), Expect = 2e-66 Identities = 160/483 (33%), Positives = 246/483 (50%), Gaps = 17/483 (3%) Query: 2 TITGNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRTT 61 T+ G +I G+ S N+ + V +PAT ++ V + V A+ A AF WS+T+ Sbjct: 6 TLDGLYINGQW--SAGNEHLRVINPATEALLTTVNGGDERAVDQAVSAATQAFADWSKTS 63 Query: 62 PLRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIKG 121 R ++ ++ + E+L + S +GK +A ++ + E+ G+ + Sbjct: 64 GAERGAILRKIATGVQANREKLMHLQSSNNGKPQFEAAIDVDDVIATFEYYAGLAEGLDA 123 Query: 122 EFSSDVGTGVDSYSLM---QPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALA 178 + S V D +S +P GVV I P+NFP + W ALA G VLKP + Sbjct: 124 KQDSAVELPTDDFSARLRREPCGVVGLIVPWNFPMVTTAWKLAPALAAGCCVVLKPSEVT 183 Query: 179 PTAAVRLAELLKEAGLPDGVFNVVHCSNEDA--EQLYRDPRIAAVSFVGSSGVAEHIYKT 236 P + LA ++ EAG+P GVFN+V C A L DPRIA VSF GS+ V + + Sbjct: 184 PLPELELAAIIAEAGVPAGVFNLV-CGTGLAVGAPLSADPRIAKVSFTGSNAVGVQVMQR 242 Query: 237 ASAYGKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETAD 296 A+ K V K+ +V+ DAD + V GG F +AG+ C A V+ V DE AD Sbjct: 243 AAETVKGVSLELGGKSSLLVLADADPELAVEVACGGGFFNAGQMCSATSRVL-VADELAD 301 Query: 297 KLIARLKPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRK 356 + + R+K E+++V EMG +V+ ++VLG+ID+G+S GA LV G + Sbjct: 302 EFLNRVKARAEAIRVADPF---DPNVEMGALVNQAQYQRVLGHIDRGLSAGAKLVCGGNR 358 Query: 357 PQVPGFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGS 416 P GY++ T+F V + +W EEIFGPV+ + R A A+ L N +FG + Sbjct: 359 PA--DLPRGYFLQPTVFTEVPLDSALWNEEIFGPVICVRRFASEAEAIALANDSQFGLVA 416 Query: 417 AVFTSNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYT 476 +V T N TA + +QAG+V +N P V ++GG+K+S G GP G++ + Sbjct: 417 SVVTRNAQTADRVANALQAGLVWINAP-QVIFPQTAWGGYKQSSIG--RELGPWGLQAFQ 473 Query: 477 RMK 479 +K Sbjct: 474 EIK 476 Lambda K H 0.319 0.135 0.404 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: 558 Number of extensions: 21 Number of successful extensions: 6 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: 501 Length of database: 482 Length adjustment: 34 Effective length of query: 467 Effective length of database: 448 Effective search space: 209216 Effective search space used: 209216 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