Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__MR1:200453 Length = 482 Score = 294 bits (752), Expect = 5e-84 Identities = 171/472 (36%), Positives = 258/472 (54%), Gaps = 4/472 (0%) Query: 1 MQHKLLINGELVSGEG-EKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTT 59 ++ + ING+ E + NPATG V+ + + AA+ AA+AA W T Sbjct: 9 LRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALT 68 Query: 60 PKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLN 119 K R L + +++ EN A L + GKPL A E+ +FA A+ + Sbjct: 69 AKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEA-KGEVTYAASFIEWFAEEAKRIY 127 Query: 120 GLAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPL 179 G + M+ + P+GV A+I PWN+P M K APALAAG +V+KP+ TP Sbjct: 128 GDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPF 187 Query: 180 TALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS 238 TAL LA LA+ PAGV +++ G +G+ + +P VR +S TGS G +++ A Sbjct: 188 TALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQCAP 247 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 ++K+ +ELGG AP IVFDDA+I+A VEG Y NAGQ C A RIY Q G+YD E Sbjct: 248 TLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAE 307 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY 358 KL AVA LK G GPL + A +E+V +E+A G V+ GG+ + G Sbjct: 308 KLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKG-ATVLAGGKVHELGGN 366 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 ++ PT+L A + + ++E FGP+ + F++ + V+ AND+++GLA+ + +D+ Sbjct: 367 FFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLV 426 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 +V+ L+YG VNT + P GG K SG G++ S YG+E+Y ++++ Sbjct: 427 WKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYI 478 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: 515 Number of extensions: 23 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: 482 Length adjustment: 34 Effective length of query: 440 Effective length of database: 448 Effective search space: 197120 Effective search space used: 197120 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 Apr 09 2024. 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