Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012386248.1 BIND_RS16960 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000019845.1:WP_012386248.1 Length = 492 Score = 216 bits (550), Expect = 2e-60 Identities = 152/470 (32%), Positives = 218/470 (46%), Gaps = 15/470 (3%) Query: 42 IGGEWVDTKER-MVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100 I G W+ + V++ A V+G G E A+ AA KA W ++R++ Sbjct: 22 IDGRWLSVGDGPSVTVENPATGTVLGHVPAFGAKETALAIAAAKKAQPAWAKKTAKERAK 81 Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160 +L LM + +L + E GK E+ ++A A FIE++A R Y V Sbjct: 82 ILRHLFDLMLENQEDLARIMTAEQGKPLTESRGEIAYAAGFIEWFAEEGKRV-YGDVIPE 140 Query: 161 PYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVF 220 PG P+G I PWNFP A+ T A G I +PA + Sbjct: 141 HLPGRRLIVRKEPIGVFAAITPWNFPSAMITRKAGPGWAAGCAGILRPASQTPFSALALG 200 Query: 221 EIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQT 280 + AG P G+ N + G G E+GA L +P R +FTGS EVG K+ LA Sbjct: 201 VLAERAGLPAGICNIVTGPGSEIGAELTGNPDVRKFSFTGSTEVGAKL------LAQCAP 254 Query: 281 WFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLE 340 K+ +E GG IV + AD D A +G + S Y GQ C A+RL++ G Y+ + Sbjct: 255 TIKKTSMELGGNAPFIVFDDADLDAAVKGAIASKYRNAGQTCVCANRLLVQDGVYDVFAQ 314 Query: 341 RVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEGEGYF 398 ++++ + L VG EE +GP++ KV +++ + G ++LGG G F Sbjct: 315 KLVEAVKALKVGDGFEEGVIIGPLIDQAALTKVDAHVADAVSLGASVILGGAPHPLGGTF 374 Query: 399 IAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLE 458 PT+ +VPPKARI EE FGPV + R + EA+ +ANDTP+GL YSR + Sbjct: 375 YEPTILADVPPKARIFHEETFGPVAPLFRFRTEEEAVTLANDTPFGLASYFYSRDIGRIM 434 Query: 459 WARREFHVGNLYFNRKITGALVGVQPFGGFKLSG---TNAKTGALDYLRL 505 G + N + V PFGG K SG +K G DYL + Sbjct: 435 RVAEGLEYGIVGINEGLIS--TEVAPFGGVKNSGIGREGSKYGIEDYLEI 482 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: 616 Number of extensions: 35 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: 516 Length of database: 492 Length adjustment: 34 Effective length of query: 482 Effective length of database: 458 Effective search space: 220756 Effective search space used: 220756 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 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