Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011842384.1 RSPH17029_RS17490 aldehyde dehydrogenase family protein
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >NCBI__GCF_000015985.1:WP_011842384.1 Length = 791 Score = 234 bits (597), Expect = 8e-66 Identities = 156/493 (31%), Positives = 244/493 (49%), Gaps = 22/493 (4%) Query: 7 VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66 +GHYIDG ++ A + V NPATG + AR+ A + ++AAVA+A AAF WS+ Sbjct: 33 LGHYIDGAFTGAETAAIE-VENPATGEILARIPAAGEAEIEAAVAAARAAFSGWSQLPGF 91 Query: 67 RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAH-GEVTRGIEIVEYACGAPNLLKTD 125 R+R ++ L + + + + ++GK + + +V I + G +L + Sbjct: 92 ERARYLYAIARGLQKRERFFSVLETLDNGKAIRETRTADVPLAIRHFYHHAGWAAVLGEE 151 Query: 126 FSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSAS 185 F + +PLGVC V P+NFP+++ W I AL AGN +LKP++ P + Sbjct: 152 FPGH-----------EPLGVCGQVIPWNFPMLMLAWKIAPALAAGNTVVLKPADLTPLTA 200 Query: 186 LLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGK 245 + A +L E GLP GV N+V G L++HP + ++F GST + I + GK Sbjct: 201 VAFAEMLDEIGLPRGVVNIVHGGAETGALLVRHPGVAKVAFTGSTAVGREIRRATAGSGK 260 Query: 246 RVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLL 305 + G K+ +V DADLD A + ++ + + GE C A S + + + +AKL Sbjct: 261 SLTLELGGKSPFVVCADADLDAAVEGVVEGVWFNQGEVCCAGSRLLLQEGIAERFLAKLR 320 Query: 306 PRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGF 365 R++++++G+ TDMG +V+A KA++E I EG RL + +P A G Sbjct: 321 ARMEKIRVGDPLDKSTDMGAIVSARQKARIEELIAGAAREGYRL--EQAACPLPAA--GH 376 Query: 366 FVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIA 425 FV F ++ Q EIFGP+ AVAL N +G S ++ + A Sbjct: 377 FVAPGFFADTEPAATVAQVEIFGPIAVTTTFRTVDEAVALANNTPYGLAASVWSENINAA 436 Query: 426 RAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWP 485 A I+ G+V IN + A SFGG K S FG A EGL Y R ++ R P Sbjct: 437 TELAARIRAGVVWINAS-NLFDAGASFGGMKESGFGREGA--REGLGAYLRPRT--PRGP 491 Query: 486 DSIAKGPEFSMPT 498 +++ +F+ T Sbjct: 492 EALVAPVDFTAHT 504 Score = 53.9 bits (128), Expect = 2e-11 Identities = 60/252 (23%), Positives = 102/252 (40%), Gaps = 20/252 (7%) Query: 9 HYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRR 68 +YI G Q + S V G ++ + AV +AL A W+ + R Sbjct: 520 NYIGGA-QVRPDGGASYVVRGPKGEALGLAPVSGRKDIRNAVEAALKA-KGWAANAHGRA 577 Query: 69 SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128 + F + + R D A ++ G+ S+A EV IE V + G +D Sbjct: 578 QVLFFLAENIAARAEDLAAALVQGGAGR--SEAAAEVRSLIERVFFYAG--------MAD 627 Query: 129 NIGGGID-------NWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERD 181 G I ++++PLGV + P P++ + +I + AGN + PS Sbjct: 628 KDDGRIHATKPRHLTLSVKEPLGVVGVLAPDEAPLLSLMSLILPLIAAGNRVVAVPSPAQ 687 Query: 182 PSASLLMARLLTEAGLPDGVFNVVQGDK-VAVDALLQHPDIEAISFVGSTPIAEYIHQQG 240 + + ++ + LP GV N+V GD+ + L +H ++ I + GS A + Sbjct: 688 ALLAQPLTQIFDTSDLPGGVVNLVTGDRNLLARTLAEHDAVDGIWYHGSAKGAAEVEALS 747 Query: 241 TAQGKRVQALGG 252 K+V GG Sbjct: 748 AGNLKQVWTNGG 759 Lambda K H 0.320 0.137 0.412 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: 910 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 791 Length adjustment: 38 Effective length of query: 462 Effective length of database: 753 Effective search space: 347886 Effective search space used: 347886 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 Apr 10 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