Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 234 bits (596), Expect = 7e-66 Identities = 162/484 (33%), Positives = 248/484 (51%), Gaps = 21/484 (4%) Query: 10 YLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPA--WSEQSSLR 67 ++NGH D + +P G + +VA + D AVA+A A F + WS QS ++ Sbjct: 24 FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSPVK 83 Query: 68 RSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHG-EVTRGIEIVEYACGAPNLLKTDF 126 R +VM +F ELL+ H DELA + + + GK ++ + +V + ++ A + + + Sbjct: 84 RKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDEL 143 Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186 + I R+P+GV A + P+NFP+++ W + AL GN +LKPSE+ P ++ Sbjct: 144 APTPHNEI-GMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTAI 202 Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAV-DALLQHPDIEAISFVGSTPIAEYIH-QQGTAHG 244 MA+L EAGLPDGV NV+ G V AL H D++ + F GST IA+ + G ++ Sbjct: 203 RMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSNM 262 Query: 245 KRVQALGGAKNHMIVMPDA-DLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAK 303 KRV G K+ IV DA DL AA+A A + GE C A S + V DELI Sbjct: 263 KRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIKL 322 Query: 304 LLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQ 363 ++ ++ + G+ P T G +V + V G+I AG EGA+L+ G +V Sbjct: 323 IVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGS--QVLAETG 380 Query: 364 GFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGG 423 G +V T+FD VT +M I ++EIFGPV+ ++ AVA+ N +G +T D Sbjct: 381 GVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDIS 440 Query: 424 IARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYG---EEGLRFYSRYKSV 480 A A++++ GMV IN H GG + FG + G ++ L + +Y V Sbjct: 441 KAHKTAKALRSGMVWIN---------HYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEV 491 Query: 481 MQRW 484 W Sbjct: 492 KATW 495 Lambda K H 0.321 0.137 0.415 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: 560 Number of extensions: 26 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: 500 Length of database: 498 Length adjustment: 34 Effective length of query: 466 Effective length of database: 464 Effective search space: 216224 Effective search space used: 216224 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 Apr 09 2024. 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