Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 258 bits (659), Expect = 4e-73 Identities = 169/459 (36%), Positives = 243/459 (52%), Gaps = 19/459 (4%) Query: 42 IGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRL 101 IGG W D + NPS +V+G A A + +A A+ AA AF W + R + Sbjct: 39 IGGAWTDGVRTYQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRFDI 98 Query: 102 LLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVP 161 L + RK EL L E GK EA +V A +++A ALR P EV+P Sbjct: 99 LDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALR---PGGEVMP 155 Query: 162 Y--PGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKV 219 PG E PLG +I PWNFP+AI I +A GN V+ KPAE + Sbjct: 156 SVRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWAL 215 Query: 220 FEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQ 279 +I H AG P GV N + G G +VGA L+E R ++FTGS+ G ++ AA + G Sbjct: 216 ADILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRV--AAACVPRG- 272 Query: 280 TWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVL 339 + +E GGK+ +V + AD ++A + S + GQ+C+A+SR+I+T+G ++ + Sbjct: 273 ---AKVQLEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFV 329 Query: 340 ERVLKRAERLSVGPAEE-NPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLE---- 393 ++++ + L V A + D+GPVV Q + L YI IG+ EG +L GG+ LE Sbjct: 330 AAMVEKMKTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNAD 389 Query: 394 -GEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452 G+++ P +FTE P RI +EEIFGPV+SV+R K++ EAL +ANDTP+GL G+ + Sbjct: 390 GAPGFYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATT 449 Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLS 491 +H +R G + N G V PFGG K S Sbjct: 450 SLKHATHFKRHAQAGMVMVNLPTAGVDYHV-PFGGRKSS 487 Lambda K H 0.319 0.137 0.403 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: 650 Number of extensions: 36 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: 516 Length of database: 512 Length adjustment: 35 Effective length of query: 481 Effective length of database: 477 Effective search space: 229437 Effective search space used: 229437 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 (21.7 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