Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_012469747.1 GLOV_RS08400 succinate-semialdehyde dehydrogenase I
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000020385.1:WP_012469747.1 Length = 484 Score = 733 bits (1892), Expect = 0.0 Identities = 352/483 (72%), Positives = 413/483 (85%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 M+L D L RQ Y++G W+ AD+G+TI V NPATGE++G++PKMG AETRRAIEAA+ A Sbjct: 1 MRLNDPSLLRQSCYLNGQWLAADSGKTIDVTNPATGEVLGTIPKMGTAETRRAIEAANAA 60 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 PAWR TAKERA LRRWF+LM+ENQ+DLA +MT EQGKPLAE++GEI+YAASF+EWF Sbjct: 61 WPAWRVKTAKERATILRRWFELMLENQEDLAIIMTAEQGKPLAESRGEISYAASFIEWFA 120 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EE KR+YGDTIP H DKRI+VIK+PIGV AAITPWNFPSAMITRKAGPALAAGCTMV+K Sbjct: 121 EEGKRLYGDTIPAHGRDKRIVVIKEPIGVCAAITPWNFPSAMITRKAGPALAAGCTMVVK 180 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240 PA+ TP+SALALAEL ERAGIP GVFSV+TGS+ E+G E+TSNPIVRKLTFTGSTEIG+Q Sbjct: 181 PATATPFSALALAELGERAGIPAGVFSVITGSSSEIGTEMTSNPIVRKLTFTGSTEIGKQ 240 Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300 L A+CA +KKVS+ELGGNAPFIVFDDADLDAAVEGA+ SKYRN GQTCVC NRL VQ G Sbjct: 241 LTAQCAATMKKVSMELGGNAPFIVFDDADLDAAVEGAIASKYRNTGQTCVCTNRLLVQAG 300 Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360 VYD F +KL AVAK+ +G+GL+ V GPLID +V KVEEHI DAVSKGA++ GGK Sbjct: 301 VYDLFAEKLATAVAKMRVGDGLKDDVQQGPLIDEASVQKVEEHIHDAVSKGARIALGGKR 360 Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420 H LGGTFF+PTIL DV LV+++ETFGP+AP+F+F +AE I M+NDTEFGLASYFY Sbjct: 361 HELGGTFFQPTILCDVTPQMLVAREETFGPVAPIFKFTTDAEAIKMANDTEFGLASYFYT 420 Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 RD+ RV+RVAE LEYGMVGINTGL+S E+APFGG+K SG+GREGSKYGIE++ E+KYLC+ Sbjct: 421 RDIGRVWRVAEALEYGMVGINTGLVSTEIAPFGGVKESGIGREGSKYGIEEFCEVKYLCM 480 Query: 481 GGI 483 GGI Sbjct: 481 GGI 483 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: 716 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: 484 Length adjustment: 34 Effective length of query: 449 Effective length of database: 450 Effective search space: 202050 Effective search space used: 202050 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