Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate SMc01656 SMc01656 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Smeli:SMc01656 Length = 475 Score = 603 bits (1555), Expect = e-177 Identities = 288/474 (60%), Positives = 358/474 (75%) Query: 1 MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60 M +LLI +G ++ + NP TG ++++AEAS Q+DAAV AA+ AF W QTTP Sbjct: 1 MDTQLLIGSRFEAGTEAEEHILNPRTGAGIIDLAEASHAQIDAAVDAAERAFVGWSQTTP 60 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 R+ LLK+AD IE+ FA LE+ NCGKP+++ NDE+PAI+D +RFFAGA R L+ Sbjct: 61 AERSNALLKIADAIEKEADEFAALEALNCGKPINAVKNDELPAIIDCWRFFAGAVRNLHA 120 Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 AAGEYL GHTSMIRRDP+G+V SIAPWNYPLMM AWKLAPA+ GN VV KPSE TPLT Sbjct: 121 PAAGEYLPGHTSMIRRDPIGIVGSIAPWNYPLMMMAWKLAPAIGGGNTVVFKPSEQTPLT 180 Query: 181 ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240 ALKLA L DI P GV+N++ GRG+TVG+ L HPKV MVS+TG IATG+ +++ A ++ Sbjct: 181 ALKLARLIADILPEGVVNVITGRGETVGNALINHPKVGMVSITGDIATGKKVLAAAAKTV 240 Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300 KRTH+ELGGKAPVIV+ DAD+EAVV G+RTFGYYNAGQDCTAACRIYA+ GIY+ LV L Sbjct: 241 KRTHLELGGKAPVIVYGDADLEAVVNGIRTFGYYNAGQDCTAACRIYAEAGIYEKLVADL 300 Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY 360 +AV+T++ DD E+GPL S +RV VE A HI++ TGG G+++ Sbjct: 301 TSAVSTIRYNLDDDTENEIGPLISRRQRDRVASFVERAADQKHIEITTGGRTGSDEGFFF 360 Query: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420 PT++AGA Q+D IV++EVFGPVVSVT F ++ V WANDS YGLASSVWTKD+ +A R Sbjct: 361 QPTVVAGATQEDEIVRREVFGPVVSVTRFTGKDDAVAWANDSDYGLASSVWTKDISKAMR 420 Query: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 ++RLQYGCTW+NTHFML +EMPHGG K SGYGKDMS+Y LEDYT VRH+M+ H Sbjct: 421 AASRLQYGCTWINTHFMLTNEMPHGGIKQSGYGKDMSVYALEDYTAVRHIMINH 474 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: 630 Number of extensions: 16 Number of successful extensions: 1 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: 475 Length adjustment: 33 Effective length of query: 441 Effective length of database: 442 Effective search space: 194922 Effective search space used: 194922 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: 51 (24.3 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