Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 252 bits (643), Expect = 2e-71 Identities = 167/480 (34%), Positives = 246/480 (51%), Gaps = 18/480 (3%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 YI G+++ G +P G+V + A++AA +A W ++ ERS Sbjct: 17 YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTERS 76 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIP 132 L + + M +N + LA + T + GK + E ++ +FA + G Sbjct: 77 IILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSLSE 136 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192 Q LIV +PIGV A I PWNFP M K PALAAG +VLKPA TP S + L Sbjct: 137 LDQNTVSLIV-HEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMVL 195 Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252 +EL +P GV++VV G E+G L N V K +FTGST GR +M+ ++I V Sbjct: 196 MELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENIIPV 254 Query: 253 SLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306 +LELGG +P I F DDA LDKAVEGA++ N G+ C C +R+ +Q+ +Y+ F Sbjct: 255 TLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLIQEDIYEKFI 313 Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE---- 362 K+ +KIG+ L+ G K+ +I+ +GA+VL+GG++ E Sbjct: 314 AKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPGE 373 Query: 363 ---GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419 G + +PTI K + +EE FGP+ + FK E I ++NDT +GL + + R Sbjct: 374 LGGGYYIKPTIFKGHNK-MRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVWTR 432 Query: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479 D +++V A++ G V +N APFGG K SG+GRE K + Y + K + IS Sbjct: 433 DAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNMLIS 492 Lambda K H 0.317 0.134 0.384 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: 537 Number of extensions: 32 Number of successful extensions: 7 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: 480 Length of database: 501 Length adjustment: 34 Effective length of query: 446 Effective length of database: 467 Effective search space: 208282 Effective search space used: 208282 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 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