Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::C6KEM4 (506 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 314 bits (805), Expect = 4e-90 Identities = 192/475 (40%), Positives = 271/475 (57%), Gaps = 16/475 (3%) Query: 13 FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72 +IGG W E G R V+NPATEA + +I G+ D + AVAAA+ AF +SR Sbjct: 8 YIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFD-----SFSRTS 62 Query: 73 GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYADLAEALDG 132 R L AI A+ K+R +LA + G P+ A V + + AL Sbjct: 63 VDERIALLEAILAEYKNRAGDLADAIAAEMGAPISLAK--TAQVGSGIGHLMSTINALKA 120 Query: 133 KQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSELA 192 + S + +S V+ EPIGVV LITPWN+PL KVAPALAAG T +LKPSE A Sbjct: 121 FEFSE-----QIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEA 175 Query: 193 SVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTSA 252 S I + G+P GV N++ G GP G LS H VD V+FTGST G ++ +A Sbjct: 176 PGSAAIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNA 235 Query: 253 AQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRLLLHEKIAKK 312 A+ VK V ELGGKSP ++ D+ +AV+ +F + N+GQ C A +R+L+HE A + Sbjct: 236 AETVKRVHQELGGKSPNVILPG-ADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAE 294 Query: 313 FLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGG-GRPQH 371 K ++ DP +EG +G V+++ Q+EKI+ I EGA + GG GRP Sbjct: 295 AAQIASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDG 354 Query: 372 LRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYGLAGAVISN 431 + G+F++PT+ + V M I +EE+FGPVI + +R + EAV +ANDT YGL+ AV+ Sbjct: 355 IETGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLS-AVLFG 413 Query: 432 DQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYLTVK 486 E +R++ L +G+++IN QP P+GG K+SG GRE G++GL ++ VK Sbjct: 414 SPEEVKRVAPRLRAGMVYINGGQP-DPSLPFGGYKQSGNGREHGKFGLAEFMEVK 467 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: 593 Number of extensions: 29 Number of successful extensions: 8 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: 474 Length adjustment: 34 Effective length of query: 472 Effective length of database: 440 Effective search space: 207680 Effective search space used: 207680 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 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