Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011766578.1 AZO_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000061505.1:WP_011766578.1 Length = 477 Score = 211 bits (536), Expect = 6e-59 Identities = 153/474 (32%), Positives = 229/474 (48%), Gaps = 24/474 (5%) Query: 53 GKIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARARILLKAAAILK 112 G I ++P T V + DAE A+ A AF++W + + RA + + AA LK Sbjct: 21 GFIDVMDP-STDTVFARIPEGAAADAEAAVAAAHAAFDAWSRTPLAERAGCIERIAAGLK 79 Query: 113 RRRLEACALMSIEVGK-NYAEADVEVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENG 171 R E +++ EVG A V+V + Y A + W N Sbjct: 80 ARSDELAHVIACEVGMPKKLAARVQVGGPLWHWNNYEALARSFE--------WERRVGNS 131 Query: 172 LM-SIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAG 230 L+ P+GV +I+PWNFP A ++AG VV+KP+E A + A + +I+ AG Sbjct: 132 LVVREPIGVVGAITPWNFPLNQITLKVAPALLAGCTVVLKPSEVAPINAFILAEIIEAAG 191 Query: 231 LPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIM 290 +PAGV + G G VGE L + + ++FTGS G + E+AA +K+V + Sbjct: 192 VPAGVFNLVTGYGPVVGEVLASDPRVDMVSFTGSTRAGRRVAELAAAT------VKKVAL 245 Query: 291 ELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAK 350 ELGGK +V + AD+ A+ +GQ CSA +RL+V + DE A Sbjct: 246 ELGGKSASVVLDDADLAAAVKGTVSSCLLNSGQTCSAHTRLLVPRARLDEAAQLAATAAS 305 Query: 351 ALKMGTG-EENANVTAVVNQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYYIQPT 409 A+K G E++ + +V+ +++ Y+ +EG L G A A +QGY++QPT Sbjct: 306 AMKPGPALAEDSRLGPLVSAAQRERVRDYIRRGVAEGARLACGGAEPPAELEQGYFVQPT 365 Query: 410 IVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARA 469 ++ D + +AQEEIFGPV+ VL +DA+ IAN + YGL G V + + ER Sbjct: 366 VLVCEDSRATVAQEEIFGPVLVVLPHDGDEDAIRIANDSPYGLAGAVWAGNEERALAVAR 425 Query: 470 EFEVGNLYFNRKITGAIVGVQ-PFGGYNMSGTDSKAGGPDYLSNFMQLKTVTER 522 G + I GA + PFGGY SG + G L F+Q K + R Sbjct: 426 RLRTGQV----DINGAAWNPRAPFGGYKQSGL-GRENGEYGLDEFLQYKAIQLR 474 Lambda K H 0.317 0.134 0.391 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: 541 Number of extensions: 30 Number of successful extensions: 5 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: 523 Length of database: 477 Length adjustment: 34 Effective length of query: 489 Effective length of database: 443 Effective search space: 216627 Effective search space used: 216627 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 (21.6 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