Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 304 bits (778), Expect = 5e-87 Identities = 173/457 (37%), Positives = 251/457 (54%), Gaps = 4/457 (0%) Query: 16 GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75 G PV NPA GDV+ + + + A+ AADAA W T K RA+ L + D+I Sbjct: 34 GATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVLRRWFDLIV 93 Query: 76 ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIR 135 N A + + GKPL A E+ +FA A+ L G +L + Sbjct: 94 GNADDLARILTAEMGKPLAEA-RGEVMYGASFVEWFAEEAKRLYGETIPGHLPDARIQVI 152 Query: 136 RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPA 194 R P+GVV +I PWN+P+ M K APALAAG + KP+E TPL+AL LA LA+ PA Sbjct: 153 RQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALAVLAERAGIPA 212 Query: 195 GVINIL-FGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPV 253 G+ +L +G + VR ++ TGS G +++ A +K+ MELGG AP Sbjct: 213 GLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKCSMELGGNAPF 272 Query: 254 IVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPD 313 IVFDDAD++ VEG + NAGQ C A RIY Q G+YD EKL AAV LK G Sbjct: 273 IVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAAAVEELKVGDGA 332 Query: 314 DESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDA 373 E +GPL ++ +E+V +++ +A G V+TGGE G ++ PT++ G Q+ Sbjct: 333 AEGVTIGPLINMPAVEKVQDHLDDLRAKGG-TVVTGGETHPLGGTFFTPTVVTGVTQEMK 391 Query: 374 IVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN 433 + ++E FGPV + F E++V+ AND+ +GLA + +D+GR RVS L+YG +N Sbjct: 392 VAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSEALEYGIVGIN 451 Query: 434 THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 T + P GG K SG G++ S +G+++Y ++++ Sbjct: 452 TGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYI 488 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: 552 Number of extensions: 24 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: 474 Length of database: 492 Length adjustment: 34 Effective length of query: 440 Effective length of database: 458 Effective search space: 201520 Effective search space used: 201520 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