Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= BRENDA::Q8VWZ1 (503 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 315 bits (807), Expect = 2e-90 Identities = 185/482 (38%), Positives = 272/482 (56%), Gaps = 13/482 (2%) Query: 9 QLFIDGEWRVPILNKRIPNINPSTEN-IIGDIPAATKEDVDLAVDAAKRAISRKNGRDWS 67 Q +I+G+W + + NP+ ++ I+ P + +D D AV AA++A W Sbjct: 8 QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYG-----SWR 62 Query: 68 AASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEE 127 RA Y+ + + + K+EL +L S + GKP+ EA D+ + V C Y AG Sbjct: 63 KVPAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRR 122 Query: 128 LDSKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPS 187 L Q P +P + ++ PIGV ALITPWN+P + WK PAL G ILKP+ Sbjct: 123 LFG-QTTPSEMPNKF--AMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPA 179 Query: 188 ELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIM 247 E +L EI GLP GV+N+V G+G EAG +L HP++D +SFTGSSATG+ + Sbjct: 180 EDTPACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVG 239 Query: 248 TTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIA 307 T + K V LE+GGK+ VV ED DL+ + ++G F T GQ C+ATSRLI+H I Sbjct: 240 ETCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIK 299 Query: 308 VEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGR--R 365 +F L + +++ E +GPI++ Q ++V ++ A+ EGA IL GG Sbjct: 300 EKFTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVT 359 Query: 366 PEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAV 425 LK+GYF +PTI+ +VT M++ REE+FGPV+A+ ST EEAI + NDT YGL S+V Sbjct: 360 EGQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSV 419 Query: 426 MSNDLERCERLSKALQAGIVWINCAQ-PSFIQAPWGGIKRSGFG-RELGEWGLENYLSVK 483 + D+ R + ++ GI +IN + + P+GG+K++G G RE G L+ + K Sbjct: 420 YTRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWK 479 Query: 484 QV 485 V Sbjct: 480 SV 481 Lambda K H 0.317 0.134 0.402 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: 605 Number of extensions: 29 Number of successful extensions: 4 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: 503 Length of database: 498 Length adjustment: 34 Effective length of query: 469 Effective length of database: 464 Effective search space: 217616 Effective search space used: 217616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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