Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein
Query= reanno::WCS417:GFF2142 (499 letters) >FitnessBrowser__Marino:GFF4005 Length = 471 Score = 218 bits (556), Expect = 3e-61 Identities = 161/481 (33%), Positives = 248/481 (51%), Gaps = 26/481 (5%) Query: 7 HYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRA 66 +YIN Q VS DV TG+ RV A + +A+AAA AAF W+++ R Sbjct: 7 NYINGQWVSWAGDMIDVHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLEERI 66 Query: 67 RVLFEYLHL-LRERKDDLARIIVAEHG---KVFTDAQGEVDRGIDILEFACGIPNLLKGE 122 +VL E LH L+ER ++A + E G K+ T Q + + + +P+ E Sbjct: 67 KVL-EQLHAGLKERAPEIAETVCREVGMPIKLATPIQAGMPAAVT-KSYLKLLPDFPFTE 124 Query: 123 HSDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSAS 182 S ++ P+GVV +TP+N+P+ + AIAAG T +LKPS P + Sbjct: 125 QSG------NSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTA 178 Query: 183 LFMAELLREAGLPKGVFNVVQGDKESV-DALIEHPDVKAVSFVGSTPIAQYIYETGARNG 241 +AE+L LPKGVFN+V G +V D LI+HPDV+ VSF GST I A + Sbjct: 179 FILAEILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLIAHAAADDF 238 Query: 242 KRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAAL 301 KR G K+ V++PDAD+ V + ++G+ C A++ ++ D D+ A Sbjct: 239 KRFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDE--ACE 296 Query: 302 TERAKHLRITDGRDLK--AEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEP- 358 A ++T G L+ +GP+ S +++ YI+ GVQ GA+L+ G P P Sbjct: 297 LAAAAVAKMTPGNPLEETTRLGPLSSAQQRDKVIDYIKLGVQEGAKLIAGG----PEAPE 352 Query: 359 GLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFT 418 G E G+++ AT+F +V + I +EEIFGPVL + ND AEA+K+ N ++G + ++ Sbjct: 353 GCEKGYFVKATVFGNVKPDSRIAQEEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWS 412 Query: 419 RDGNIAREFARRIEVGMVGINVPISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFYTKQKS 478 D A++ A ++ G V +N PMA FGG+ S G +G G+ + + +S Sbjct: 413 GDDAKAKKIASKLRTGQVFVNGGAFNPMA--PFGGFGHSGIG--REFGKWGLEEFLEVRS 468 Query: 479 I 479 + Sbjct: 469 L 469 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: 545 Number of extensions: 21 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: 471 Length adjustment: 34 Effective length of query: 465 Effective length of database: 437 Effective search space: 203205 Effective search space used: 203205 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