Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate H281DRAFT_03178 H281DRAFT_03178 succinate semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >FitnessBrowser__Burk376:H281DRAFT_03178 Length = 486 Score = 675 bits (1741), Expect = 0.0 Identities = 329/481 (68%), Positives = 390/481 (81%), Gaps = 2/481 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 + LKD L + A++ G W AD+G T +V NPATGE++ TVP+MG AETRRAI+AA+ A Sbjct: 4 LTLKDPALLKSHAYLAGEWQGADDGSTFEVVNPATGEVVATVPRMGTAETRRAIDAANAA 63 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 PAWRA TAK+RA LR+W++L++EN DDL ++T EQGKPLAEAKGEI YAASF+EWFA Sbjct: 64 WPAWRASTAKQRAVILRKWHDLMLENADDLALILTTEQGKPLAEAKGEIQYAASFLEWFA 123 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 EE KR+ GD IP DKR++V K+P+GV AAITPWNFPAAMITRK GPALAAGC +++K Sbjct: 124 EEGKRLNGDTIPTPANDKRIVVTKEPVGVCAAITPWNFPAAMITRKVGPALAAGCPIIVK 183 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240 PA TP SALAL LA RAG+P+GV +VVTG IG E+T NPIVRKLSFTGST +GR Sbjct: 184 PAEATPLSALALAVLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRL 243 Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300 LMA+CA +KKVSLELGGNAPFIVFDDADLD AV GAI SKYRN+GQTCVC NR Y+ D Sbjct: 244 LMAQCAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDK 303 Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359 VYDAFA KL+AAV +L +G G E G T GPLI+E AV KV+ HI DAL KGA ++ GGK Sbjct: 304 VYDAFAAKLRAAVEQLTVGRGTEAGVTQGPLINEAAVLKVESHIEDALAKGARVVTGGKR 363 Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 ++ FFEPTIL +V D VA++ETFGPLAPLFRF + EVIA++NDTEFGLASYFY+ Sbjct: 364 HALGHGFFEPTILADVTPDMKVARDETFGPLAPLFRFSSDEEVIALANDTEFGLASYFYS 423 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 RD+GRV+RVAEALEYGMVG+NTGLISNEVAPFGG+K SGLGREGS YGI+DY+ IKY+C+ Sbjct: 424 RDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKYMCV 483 Query: 479 G 479 G Sbjct: 484 G 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: 720 Number of extensions: 12 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: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 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