Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_015820919.1 TERTU_RS10425 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000023025.1:WP_015820919.1 Length = 480 Score = 186 bits (473), Expect = 1e-51 Identities = 141/472 (29%), Positives = 232/472 (49%), Gaps = 28/472 (5%) Query: 38 YPLYIGGEWVD-TKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQE 96 + ++I G W + E + S+ P A + + A A+ A+E+A AFK W++ P Sbjct: 2 HSVFIDGLWREGCGEPIRSIEP-ATGKTLWEGHSASTADVFQAVESAQVAFKPWRNMPLT 60 Query: 97 DRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPA 156 +R+ ++ A + R++EL + E GK E+ +V I+ ++ A + Sbjct: 61 ERTSVVKHFAECLLSRQQELAEIISRETGKPHWESLQEVTAMINKVDISISAQQQRAGTT 120 Query: 157 VEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216 + + P G V P+NFP + G I+ + GNTV+ KP+E Sbjct: 121 RDA------QLALTHRPHGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEKTPYTA 174 Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276 + EI+ +AG P GV+N + G G VG L++ + FTGS G+KI+ A Sbjct: 175 QRTLEIWAQAGLPAGVINLIQG-GASVGKTLIDSDINGVL-FTGSHATGVKIHRALA--- 229 Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336 G A +E GG + +IVDE + D+AA V+ SA+ GQ+C+ A RL+L E Sbjct: 230 -GHPEILLA-LELGGNNPLIVDEVDNIDVAAWHVIRSAFISTGQRCTCARRLVLIGNTGE 287 Query: 337 PVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRL---- 392 VLERV++ +L++G ++NP GP++ ++VL + + GG+ + Sbjct: 288 RVLERVIQWVPKLAIGHWQDNPFFGPLIDTMAVQQVLKI-----QDKLIAAGGEAILFAQ 342 Query: 393 EGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452 GE FI+P + + + +E+FGP+L V R ++F +A+ +ANDT +GL G+ S Sbjct: 343 PGEHAFISPGI-VRINGNKTVFDDEVFGPLLQVYRAENFTQAVALANDTRFGLAAGLLSD 401 Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTG--ALDY 502 + H E + G + N+ GA + PFGG SG + + A DY Sbjct: 402 NKAHQHIFLNESNAGVISINQPTAGASSKL-PFGGTGHSGNHRPSALYAADY 452 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: 557 Number of extensions: 20 Number of successful extensions: 4 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: 480 Length adjustment: 34 Effective length of query: 482 Effective length of database: 446 Effective search space: 214972 Effective search space used: 214972 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