Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_020309040.1 PST_RS00500 succinate-semialdehyde dehydrogenase I
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_000013785.1:WP_020309040.1 Length = 482 Score = 820 bits (2118), Expect = 0.0 Identities = 405/482 (84%), Positives = 448/482 (92%), Gaps = 2/482 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 MQLKD LFRQQA+IDGAW+DAD+GQTI VNNPATGEILGTVPKMGAAETRRAI+AA++A Sbjct: 1 MQLKDTALFRQQAYIDGAWLDADSGQTISVNNPATGEILGTVPKMGAAETRRAIDAAERA 60 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 LPAWR LTAKER+ KLRRW+ELL+ENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA Sbjct: 61 LPAWRDLTAKERSQKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 EEAKRIYGD IPGHQ DKR++VIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK Sbjct: 121 EEAKRIYGDTIPGHQKDKRILVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240 PASQTPFSALA+VELA RAGIPKGVLSVVTGSAGDIG ELT+NP VRK+SFTGSTE+G + Sbjct: 181 PASQTPFSALAMVELAERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAK 240 Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300 LM +CA IKKVSLELGGNAPFIVFDDADLD+AV+GA+ SKYRN GQTCVC NR+Y+QD Sbjct: 241 LMEQCAPGIKKVSLELGGNAPFIVFDDADLDEAVKGAMQSKYRNAGQTCVCVNRIYVQDG 300 Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKS 360 VYDAFAEK +AAVAKL++GNGLEEGT GPLID++A AKV+EHI DA+ +GA L+AGG++ Sbjct: 301 VYDAFAEKFQAAVAKLRVGNGLEEGTDIGPLIDDRAAAKVREHIEDAVAQGARLVAGGQA 360 Query: 361 --MEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 M G++FEPT+LV+VP A VAKEETFGPLAPLFRFKDEAE I+ +NDTEFGLASYFYA Sbjct: 361 HQMGGSYFEPTVLVDVPDSAKVAKEETFGPLAPLFRFKDEAEAISKANDTEFGLASYFYA 420 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 RDLGRVFRVAEALEYGMVG+NTGLIS EVAPFGG+K+SGLGREGSKYGIEDYLEIKYLC+ Sbjct: 421 RDLGRVFRVAEALEYGMVGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYLCM 480 Query: 479 GI 480 GI Sbjct: 481 GI 482 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: 803 Number of extensions: 17 Number of successful extensions: 2 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: 482 Length adjustment: 34 Effective length of query: 446 Effective length of database: 448 Effective search space: 199808 Effective search space used: 199808 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: 51 (24.3 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