Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Phaeo:GFF2918 Length = 491 Score = 300 bits (768), Expect = 7e-86 Identities = 176/472 (37%), Positives = 253/472 (53%), Gaps = 4/472 (0%) Query: 1 MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60 ++ + I G V G V NPA GDV+ +A+ S QV A+ A+ A +W + T Sbjct: 18 LEPRAYIGGAFVDGADGTFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQKDWAKWTG 77 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 K RA L K D++ EN + A + + GKPL + EI FFA A+ + G Sbjct: 78 KERANVLRKWFDLMMENQEDLAVILTAEMGKPLAES-RGEIGYGASFIEFFAEEAKRIYG 136 Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 + + + P+GV ASI PWN+P M K PALAAG V +P+E+TPL+ Sbjct: 137 ETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARPAELTPLS 196 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKT-VGDPLTGHPKVRMVSLTGSIATGEHIISHTAS 238 A LA LA PAGV N++ + G + VR ++ TGS G ++ A Sbjct: 197 ATALAVLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRILMRQAAD 256 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 ++ + MELGG AP IVFDDAD++A VEG + N GQ C A RIY Q G+YD Sbjct: 257 TVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAGVYDAFAA 316 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY 358 KL AVA + G E T+ GPL + +E+V + +AK G +VI GG + G Sbjct: 317 KLKEAVAKMTVGDGLAEGTQFGPLINEKAVEKVQAHIADAKEKG-AEVILGGNPSELGGT 375 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 ++ PT++ GA QD Q E FGP+ + F+ E+ V+ AND+ +GLAS + KD+ R Sbjct: 376 FFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYAKDLSRV 435 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 ++V+ L+YG VNT + P GG K SG G++ S +G+EDY ++++ Sbjct: 436 YKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYI 487 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: 502 Number of extensions: 22 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: 491 Length adjustment: 34 Effective length of query: 440 Effective length of database: 457 Effective search space: 201080 Effective search space used: 201080 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