Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= reanno::WCS417:GFF2142 (499 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 200 bits (508), Expect = 2e-55 Identities = 139/443 (31%), Positives = 204/443 (46%), Gaps = 14/443 (3%) Query: 4 TIEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPI 63 T+ YI + V+ D E + A R + +A+AAA+ A W DT P Sbjct: 511 TVPLYIGGRDVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPA 570 Query: 64 RRARVLFEYLHLLRERKDDLARIIVAEHGKVFTDAQGEVDRGIDILEFACGIPNLLKGEH 123 RA L + R+R +L+ V E GK + A +V GID LE+ L Sbjct: 571 DRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPR 630 Query: 124 SDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASL 183 + G N QP G+ A + P+NFP + + M AI GN I KPS Sbjct: 631 RMGRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGY 690 Query: 184 FMAELLREAGLPKGVFNVVQGDKESV-DALIEHPDVKAVSFVGSTPIAQYIYE------T 236 +AE+ REAGLP+GVFN G + D L+EHPD+ + F GS + I E Sbjct: 691 NLAEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQP 750 Query: 237 GARNGKRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDK 296 G R KRV G KN ++ DAD+++ V ++ +A+G G++C A S +++ + D+ Sbjct: 751 GQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDR 810 Query: 297 VIAALTERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPT 356 I L + A + I D MGP+ + +S YI + G LL R +P Sbjct: 811 FIERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLL--KRTDLPA 868 Query: 357 EPGLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSC 416 E G ++ T+ + E I +EEIFGPVLA +R F EA+ + N F + Sbjct: 869 E-----GCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAV 923 Query: 417 FTRDGNIAREFARRIEVGMVGIN 439 F+R + R VG + +N Sbjct: 924 FSRSPEHLDKARREFRVGNLYLN 946 Lambda K H 0.320 0.136 0.407 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: 1072 Number of extensions: 56 Number of successful extensions: 5 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: 499 Length of database: 1006 Length adjustment: 39 Effective length of query: 460 Effective length of database: 967 Effective search space: 444820 Effective search space used: 444820 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: 54 (25.4 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