Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_084200632.1 C0029_RS01440 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_002869505.1:WP_084200632.1 Length = 487 Score = 654 bits (1688), Expect = 0.0 Identities = 307/483 (63%), Positives = 394/483 (81%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 + L D L + QAY++G WVDAD+G T V NPATGE+I + ++GAAET RAI AAD A Sbjct: 3 LTLSDPTLLKHQAYINGEWVDADDGATFAVTNPATGEVITEIARVGAAETARAIAAADTA 62 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 + W+ + AK RA LR+WFDLM+E+Q+DLA+LMT EQGK +AE++GEIAY A+F+EWFG Sbjct: 63 MADWKKVPAKARAQVLRKWFDLMMEHQEDLAQLMTAEQGKVIAESRGEIAYGAAFIEWFG 122 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EEAKRI GD IPG DKRI+ IKQP+GV AAITPWNFP+AMI RKA PALAAGC++V+K Sbjct: 123 EEAKRIDGDVIPGPSSDKRIVCIKQPVGVVAAITPWNFPNAMIARKAAPALAAGCSIVIK 182 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240 PAS+TP SALA+AELAERAG+P GV +VV GSA ++G E+TSNP VRKLTFTGST IG+ Sbjct: 183 PASETPLSALAMAELAERAGVPAGVVNVVAGSASKIGAEITSNPTVRKLTFTGSTPIGKM 242 Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300 L+ +CA +KK S+ELGGNAPFIVFDDAD+D+A+ GA+ISKYRN GQTCVC+NR++VQDG Sbjct: 243 LVEQCAPTMKKTSMELGGNAPFIVFDDADIDSAITGAMISKYRNAGQTCVCSNRIFVQDG 302 Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360 VYD FV K A A+L +GNG + GV GPL+ KA+ V++ + +++++GA+V +GG Sbjct: 303 VYDEFVAKFVKATAELTVGNGADDGVVIGPLVTEKAMNDVDKLVQESIAQGAQVAAGGSA 362 Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420 H+LGG+F++PT+L +V + V ++E FGP++PV RF E EVIAM+NDTEFGLASYFY Sbjct: 363 HSLGGSFYQPTVLTEVTSDMAVFRNEIFGPVSPVVRFSTEEEVIAMANDTEFGLASYFYT 422 Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 RD+ RV+R+AE L+YG+VGIN G+ISNE+APFGG+K SG GREGSKYGI+DY+EIKY+ + Sbjct: 423 RDIGRVWRIAEALDYGIVGINEGIISNEMAPFGGVKESGSGREGSKYGIDDYVEIKYMLM 482 Query: 481 GGI 483 GG+ Sbjct: 483 GGL 485 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: 692 Number of extensions: 16 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: 487 Length adjustment: 34 Effective length of query: 449 Effective length of database: 453 Effective search space: 203397 Effective search space used: 203397 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 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