Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate H281DRAFT_03178 H281DRAFT_03178 succinate semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_03178 Length = 486 Score = 697 bits (1798), Expect = 0.0 Identities = 341/483 (70%), Positives = 399/483 (82%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 + LKD L + AY+ G W AD+G T +V NPATGE++ +VP+MG AETRRAI+AA+ A Sbjct: 4 LTLKDPALLKSHAYLAGEWQGADDGSTFEVVNPATGEVVATVPRMGTAETRRAIDAANAA 63 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 PAWRA TAK+RA LR+W DLM+EN DDLA ++T EQGKPLAEAKGEI YAASFLEWF Sbjct: 64 WPAWRASTAKQRAVILRKWHDLMLENADDLALILTTEQGKPLAEAKGEIQYAASFLEWFA 123 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EE KR+ GDTIP DKRI+V K+P+GV AAITPWNFP+AMITRK GPALAAGC +++K Sbjct: 124 EEGKRLNGDTIPTPANDKRIVVTKEPVGVCAAITPWNFPAAMITRKVGPALAAGCPIIVK 183 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240 PA TP SALALA LAERAG+P+GVF+VVTG +G E+T NPIVRKL+FTGST +GR Sbjct: 184 PAEATPLSALALAVLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRL 243 Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300 LMA+CA +KKVSLELGGNAPFIVFDDADLDAAV GA+ SKYRN+GQTCVC NR YV D Sbjct: 244 LMAQCAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDK 303 Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360 VYDAF KL+AAV +L +G G EAGVT GPLI+ AV KVE HI DA++KGA+VV+GGK Sbjct: 304 VYDAFAAKLRAAVEQLTVGRGTEAGVTQGPLINEAAVLKVESHIEDALAKGARVVTGGKR 363 Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420 HALG FFEPTIL DV + V++DETFGPLAP+FRF + EVIA++NDTEFGLASYFY+ Sbjct: 364 HALGHGFFEPTILADVTPDMKVARDETFGPLAPLFRFSSDEEVIALANDTEFGLASYFYS 423 Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 RD+ RV+RVAE LEYGMVGINTGLISNEVAPFGG+K SGLGREGS YGI+DY+ IKY+C+ Sbjct: 424 RDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKYMCV 483 Query: 481 GGI 483 GGI Sbjct: 484 GGI 486 Lambda K H 0.317 0.135 0.391 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: 739 Number of extensions: 12 Number of successful extensions: 1 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: 483 Length of database: 486 Length adjustment: 34 Effective length of query: 449 Effective length of database: 452 Effective search space: 202948 Effective search space used: 202948 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