Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_010961010.1 MCA_RS08650 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000008325.1:WP_010961010.1 Length = 491 Score = 221 bits (562), Expect = 6e-62 Identities = 156/475 (32%), Positives = 223/475 (46%), Gaps = 19/475 (4%) Query: 42 IGGEWVDTKE-RMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100 I G+WVD + S+ A + G AE A+ AA A+ W+ ++R+ Sbjct: 19 IDGQWVDADHSKTFSVTDPATGRALADVPAMGAAETMRAIAAAEHAWTGWRGKTAKERAA 78 Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160 +L + L+ +L L E GK EA ++ A F+E++A A R E + Sbjct: 79 VLRRWYELILSHTEDLARILTAEQGKPLTEARNEIGYAAGFVEWFAEEAGR---AYGETI 135 Query: 161 PYPGEDNESFYV--PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAK 218 P P D + P+G I PWNFP A+ T I +A G TV+ KPAE + Sbjct: 136 PSPVPDKRLLVIRQPIGVCAAITPWNFPAAMITRKIAPALAAGCTVVVKPAEQTPLTALA 195 Query: 219 VFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPG 278 + ++ +AGFPPGV+N + G E +G L +P R ++FTGS EVG + +A Sbjct: 196 LADLAVQAGFPPGVINVVTGDPEAIGGELTSNPLIRKLSFTGSTEVGRLL------MAQC 249 Query: 279 QTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPV 338 K+ +E GG IV E AD D A EG ++S Y GQ C +R ++ Y+ Sbjct: 250 AATVKKISLELGGNAPFIVFEDADLDAAVEGALLSKYRNTGQTCVCTNRFLIQDSIYDAF 309 Query: 339 LERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVL-GGKRLEGEG 396 ER+ + RL VG +E GP++ + KV +I + G VL GG R G Sbjct: 310 AERLAAKVRRLEVGNGLDEGVVQGPLIDEQALAKVERHIADALDRGARVLAGGGRHPLGG 369 Query: 397 YFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREH 456 F PTV +V P+ +EE FGPV ++R EAL +AN T YGL Y+R Sbjct: 370 RFFQPTVLVDVTPEMLCTREETFGPVAPLLRFGSEEEALAIANATEYGLAAYFYTRDLAR 429 Query: 457 LEWARREFHVGNLYFNRKITGAL-VGVQPFGGFKLSGTNAKTGALDYLRLFLEMK 510 G + N TG L V PFGG K SG + G+ + +LE+K Sbjct: 430 AFRVGEALEYGMVGIN---TGMLSYDVAPFGGVKQSGI-GREGSHHGMDEYLELK 480 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: 589 Number of extensions: 33 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: 491 Length adjustment: 34 Effective length of query: 482 Effective length of database: 457 Effective search space: 220274 Effective search space used: 220274 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