Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate RR42_RS21375 RR42_RS21375 succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >FitnessBrowser__Cup4G11:RR42_RS21375 Length = 488 Score = 684 bits (1766), Expect = 0.0 Identities = 342/484 (70%), Positives = 393/484 (81%), Gaps = 5/484 (1%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 MQLKD L R QAFI G W AD+G T V NPA G ++GTVP MGAAET RAIEAA A Sbjct: 1 MQLKDPTLLRSQAFIGGQWQSADSGATFPVTNPADGSLIGTVPLMGAAETTRAIEAARVA 60 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 AWR TA+ERA LR WY+L++ N DDL LMT EQGKPLAEA+GE YAASF+EWFA Sbjct: 61 QAAWRRKTARERAQVLRAWYDLMLANADDLAVLMTTEQGKPLAEARGEAVYAASFLEWFA 120 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 E+AKR++GDV+ DKRL+V+K+P+GV AAITPWNFP AMITRKAGPALAAGC MV+K Sbjct: 121 EQAKRVHGDVLATPASDKRLLVVKEPVGVCAAITPWNFPLAMITRKAGPALAAGCAMVLK 180 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAG---DIGGELTSNPIVRKLSFTGSTEI 237 PA TP SALAL LA RAG+P G+LSVVTG A +IG ELT +P+VRKLSFTGSTE+ Sbjct: 181 PAEDTPLSALALALLAERAGLPAGLLSVVTGDAASSIEIGAELTGSPVVRKLSFTGSTEV 240 Query: 238 GRQLMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYI 297 GR LM + A IKK+SLELGGNAPFIVFDDADLD AVEGA+ SKYRN GQTCVCANRLY+ Sbjct: 241 GRILMRQSAPTIKKLSLELGGNAPFIVFDDADLDAAVEGAMASKYRNAGQTCVCANRLYV 300 Query: 298 QDSVYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAG 357 D VYDAFA+KL AAV LK+G+GLE G GPLI+E AVAKV++HIADAL KGA LL G Sbjct: 301 HDKVYDAFAQKLVAAVKTLKVGHGLEPGVQQGPLINEDAVAKVEQHIADALGKGARLLTG 360 Query: 358 GK--SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASY 415 GK + G FFEPT+L NV D VAK+ETFGPLAPLFRF + EV+ M+NDTEFGLASY Sbjct: 361 GKRHDLGGTFFEPTVLANVTPDMVVAKQETFGPLAPLFRFTSDEEVVNMANDTEFGLASY 420 Query: 416 FYARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 475 F++RD+GR++RVAEALEYGMVG+NTGLISNEVAPFGG+K SGLGREG+ YGIE+YLE+KY Sbjct: 421 FFSRDIGRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGASYGIEEYLEVKY 480 Query: 476 LCLG 479 LC+G Sbjct: 481 LCMG 484 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: 726 Number of extensions: 16 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: 488 Length adjustment: 34 Effective length of query: 446 Effective length of database: 454 Effective search space: 202484 Effective search space used: 202484 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 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