Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::C6KEM4 (506 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 331 bits (849), Expect = 3e-95 Identities = 190/497 (38%), Positives = 285/497 (57%), Gaps = 21/497 (4%) Query: 13 FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72 FIGG W P G+ +P IP A+D+E+A+ AA A +D W + Sbjct: 22 FIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAA--KDA---WGKTS 76 Query: 73 GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEA-SGDMDDVAACFEYYADLAEALD 131 R+N L IA +++ LA+ ET ++GK + E + D+ F Y+A A + Sbjct: 77 VTERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQE 136 Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191 G N SY EP+GVVG I PWN+PLLMA WK+APALAAG +LKP+E Sbjct: 137 GSAADIDG----NTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQ 192 Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251 VS L L + ++ LPPGVLN++ G G EAG L++ + K+AFTGSTE G I+ Sbjct: 193 TPVSILVLLELIEDL-LPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHILKC 251 Query: 252 AAQMVKPVSLELGGKSPLIVFDDIGD-----IDKAVEWTMFGIFANAGQVCSATSRLLLH 306 AA+ + P ++ELGGKSP + F D+ D +DKAVE + F N G+VC+ SR+L+ Sbjct: 252 AAESLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGMLLAFF-NQGEVCTCPSRVLIQ 310 Query: 307 EKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGG 366 E I +F+++++A A+ IK +PL+ ++G+ S+ Q++KI +++ + EGA +L GG Sbjct: 311 ESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGG 370 Query: 367 GRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423 Q +G+++ PTI+ M+I+QEE+FGPVI V F+ ++EA+ +ANDT YG Sbjct: 371 SLCQLEGEQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYG 429 Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYL 483 L V + D R +R+ + + +G +WINC A +GG K+SG GRE + L++Y Sbjct: 430 LGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQ 489 Query: 484 TVKQVTKYCSDEPWGWY 500 K + P G++ Sbjct: 490 NTKNLLVSYDINPLGFF 506 Lambda K H 0.318 0.136 0.418 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: 656 Number of extensions: 27 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: 506 Length of database: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 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 (21.7 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