Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 203 bits (516), Expect = 1e-56 Identities = 151/478 (31%), Positives = 231/478 (48%), Gaps = 10/478 (2%) Query: 10 YLNGH-VQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRR 68 Y++G V+ +R +V NPAT V RVAL A+ +A AFPAW+ R Sbjct: 8 YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAER 67 Query: 69 SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128 ++ K +R DE+A+ IS E G L + + A +L KT + Sbjct: 68 LEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKT-ALSLAKTYAFE 126 Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188 G +++P+GV + +TP+N+P+ + AL AG +LKPSE P ++ ++ Sbjct: 127 RRQG--TTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPYSARIL 184 Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALL-QHPDIEAISFVGSTPIAEYIHQQGTAHGKRV 247 A ++ EAG+P GVFN+V GD + +L HP ++ +S GS + ++G A K+V Sbjct: 185 AEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAATIKKV 244 Query: 248 QALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPR 307 G K+ I+ AD +A + A G+ G+ C A S DE Sbjct: 245 SLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEGLAAEL 304 Query: 308 IDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFV 367 Q+K+G+ P T MGP+ KV I G+ EGA+L+ G + G ++G+FV Sbjct: 305 CAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPE-RPEGLDKGYFV 363 Query: 368 GATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARA 427 T+F +VT M+I ++EIFGPVL + D AVA N +G + D ARA Sbjct: 364 RPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYAGDLDEARA 423 Query: 428 FARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWP 485 AR ++ GMV +N + P FGG ++S G +GE G + K++ P Sbjct: 424 VARRLRTGMVHLNGALSHPGG--PFGGIRQS--GVGREWGEAGFEEFLESKTLFGSEP 477 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: 537 Number of extensions: 38 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: 500 Length of database: 479 Length adjustment: 34 Effective length of query: 466 Effective length of database: 445 Effective search space: 207370 Effective search space used: 207370 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