Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase
Query= BRENDA::Q4DRT8 (561 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15035 Length = 496 Score = 135 bits (339), Expect = 5e-36 Identities = 129/438 (29%), Positives = 194/438 (44%), Gaps = 32/438 (7%) Query: 92 IDTALQASRE------WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKSPFQAE 145 +D A+ ++R+ WS S +R + L A LI R EL L K A Sbjct: 57 VDAAVISARQAFESGVWSARSPGERKQVLLRLAELIMAN-REELALLDSLNMGKPVMDAY 115 Query: 146 IDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEGFVSTIAPFNFAAIAA 205 + + R+ + LY DQ ++PS+ V ++ L G V+ + P+NF A Sbjct: 116 TIDVPGAAGVFRWYAESLDKLY-DQ-IAPSAQNVLATITREAL-GVVAAVVPWNFPLDMA 172 Query: 206 NLVACPALM-GNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEPDVMTNFVNSH 264 PAL GN V+ KP+ + S L ++ EAG+P GV+N LP + + H Sbjct: 173 AWKLAPALAAGNSVILKPAEQSPFSALRLGELALEAGVPPGVLNVLPGLGEQAGKALGLH 232 Query: 265 RDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHPSA-DLKLAAAL 323 D+ + FTGST+V + + + N+ ++ E GGK +LV DL LAA Sbjct: 233 LDIDCLVFTGSTEV-----GKYFMQYSAQSNLKQVWLECGGKSANLVFADCQDLDLAAQK 287 Query: 324 TVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKSFMCAVIDETA 383 G F QG+ CSA SRL +S +E ++ E+ + G P D S A++D Sbjct: 288 AAFGIFFNQGEVCSANSRLLVERSIHDEFVERLMVQVERWQPGDPLDSSSTAGAIVDSRQ 347 Query: 384 FERNKKYIDIAKSSPSTYSVIAGGGYDKTEGW--FVQPTIVESKDSQAQLMHEEIFGPIL 441 R K+I A+ + + GG G F+QPTI + L +E+FGP+L Sbjct: 348 TARIMKFIQQAERQGA--KRVCGGQQSIINGSDNFIQPTIFTGVTADMPLFRDEVFGPVL 405 Query: 442 TVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAAGNYYINDK 501 V +DD + + N S Y L S++ D + LR AG +N Sbjct: 406 AVTAFDDE-----ASALQLANDSV-YGLAASLWTDDLNRAH-RVARQLR--AGTVSVNS- 455 Query: 502 CTGAVVGQQPFGGARASG 519 A+ PFGG + SG Sbjct: 456 -VDALDVTVPFGGGKQSG 472 Lambda K H 0.320 0.133 0.402 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: 596 Number of extensions: 25 Number of successful extensions: 3 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: 561 Length of database: 496 Length adjustment: 35 Effective length of query: 526 Effective length of database: 461 Effective search space: 242486 Effective search space used: 242486 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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