Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_076477023.1 BW971_RS04825 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_900156495.1:WP_076477023.1 Length = 500 Score = 402 bits (1033), Expect = e-116 Identities = 210/466 (45%), Positives = 278/466 (59%), Gaps = 2/466 (0%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66 + G G G V PAT +V+ ++ A+A VD AV AA A W TP R+ Sbjct: 16 VEGAEFRGSGPLHRVIAPATDEVVATMSLATAADVDTAVAAARRALPAWSGATPAQRSTV 75 Query: 67 LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126 LL A V++ A E + GK + A ++P +D FFAG AR L G A EY Sbjct: 76 LLDFARVLDREAHALAVQEVSHTGKTIRLASEFDVPGSIDNVTFFAGVARDLVGKATAEY 135 Query: 127 LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE 186 HTS IRR+ +GVV SI PWNYP+ MA WK PA+AAG +VLKP+EITPLT + LA Sbjct: 136 SPDHTSSIRREAVGVVGSITPWNYPIQMAVWKALPAIAAGCTLVLKPAEITPLTTITLAR 195 Query: 187 LAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHM 245 LA + P GV N+L G G VG L GHP V +V+ TGS G +++ A R + Sbjct: 196 LASEAGLPDGVFNVLTGTGAEVGAALAGHPGVDLVTFTGSTGVGRQVMAQAAVHGTRVQL 255 Query: 246 ELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVA 305 ELGGKAP +VFDDAD+EA V G NAGQDCTAA R +YD V + +A Sbjct: 256 ELGGKAPFVVFDDADLEAAVHGAVAGSLINAGQDCTAATRAIVAPALYDDFVSGVAELMA 315 Query: 306 TLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLL 365 ++ G P D +T++G LSS H E+V V+ A+ TG I+V+TGG G G +Y PTLL Sbjct: 316 GVRVGDPTDPATDMGSLSSRHHREKVAAMVDRARDTG-IRVVTGGHVPDGPGAFYPPTLL 374 Query: 366 AGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARL 425 A + + + E+FGPV++V+ F +++ + A D+ YGLA+S WT+DV RA R S + Sbjct: 375 ADVGEGAEVYRDEIFGPVLTVSSFTDDDDALRRAGDTVYGLAASAWTRDVYRAQRASREI 434 Query: 426 QYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVM 471 + GC W+N H +VSEMPHGG + SG+GKDMS Y +++Y V HVM Sbjct: 435 RAGCVWINDHIPIVSEMPHGGLRASGFGKDMSTYSMDEYLTVEHVM 480 Lambda K H 0.317 0.134 0.397 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: 590 Number of extensions: 17 Number of successful extensions: 3 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: 474 Length of database: 500 Length adjustment: 34 Effective length of query: 440 Effective length of database: 466 Effective search space: 205040 Effective search space used: 205040 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 24 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