Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_011841815.1 RSPH17029_RS13480 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_000015985.1:WP_011841815.1 Length = 492 Score = 659 bits (1700), Expect = 0.0 Identities = 320/481 (66%), Positives = 386/481 (80%), Gaps = 3/481 (0%) Query: 3 LKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP 62 LKD L +AF+ G WVDAD+G T +V NPA G+++ TVP +G AET RAI AA++A+ Sbjct: 12 LKDPSLLETRAFVAGEWVDADDGATFEVTNPARGDVICTVPDLGRAETARAIAAAEEAMK 71 Query: 63 AWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEE 122 W A T KERA +R+W++L++ NQDDLG ++T E GKPLAEAKGEIAY ASFIEWF EE Sbjct: 72 EWAARTGKERAQVMRKWFDLMMANQDDLGAILTAEMGKPLAEAKGEIAYGASFIEWFGEE 131 Query: 123 AKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPA 182 AKRIYG+ IPGH DKR+ V+KQPIGV +ITPWNFP AMITRK GPALAAGC V +PA Sbjct: 132 AKRIYGETIPGHMRDKRITVLKQPIGVVGSITPWNFPNAMITRKCGPALAAGCGFVARPA 191 Query: 183 SQTPFSALALVELAHRAGIPKGVLSVVTGS-AGDIGGELTSNPIVRKLSFTGSTEIGRQL 241 ++TP SALAL L RAG+PKG+LSV+T S + DIG E+ NPIVRKL+FTGSTE+GR L Sbjct: 192 AETPLSALALAVLGERAGLPKGILSVITSSRSSDIGKEMCENPIVRKLTFTGSTEVGRIL 251 Query: 242 MAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSV 301 + + A + K S+ELGGNAPFIVFDDADLD AV+GA+ SK+RNNGQTCVCANR+Y+Q V Sbjct: 252 LRQAADQVMKCSMELGGNAPFIVFDDADLDAAVQGAMASKFRNNGQTCVCANRIYVQSGV 311 Query: 302 YDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK-- 359 YDAFAEKL AAV KLK+G+GL EGT GPLI+EKAVAKV+EHI D L G +L GGK Sbjct: 312 YDAFAEKLAAAVKKLKVGDGLVEGTEAGPLINEKAVAKVEEHIRDVLDGGGQVLTGGKRH 371 Query: 360 SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419 ++ G FFEPT++ V ++ V+ EETFGPLAPLFRF+ E E + +NDT FGLASYFYAR Sbjct: 372 ALGGTFFEPTVVTGVKQEMKVSTEETFGPLAPLFRFETEEEAVGYANDTIFGLASYFYAR 431 Query: 420 DLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479 D+GR+ RV EALEYG+VGVNTG+IS EVAPFGG+K SGLGREGS++GIEDYLE+KY+CL Sbjct: 432 DVGRITRVQEALEYGIVGVNTGIISTEVAPFGGVKQSGLGREGSRHGIEDYLEMKYICLS 491 Query: 480 I 480 I Sbjct: 492 I 492 Lambda K H 0.317 0.135 0.390 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: 698 Number of extensions: 12 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: 480 Length of database: 492 Length adjustment: 34 Effective length of query: 446 Effective length of database: 458 Effective search space: 204268 Effective search space used: 204268 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. 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