Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_023434135.1 N177_RS19425 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000496075.1:WP_023434135.1 Length = 489 Score = 654 bits (1686), Expect = 0.0 Identities = 316/482 (65%), Positives = 393/482 (81%), Gaps = 3/482 (0%) Query: 2 QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61 +LKDA L + Q YV+G WV I V NPATGE + SVP+ G AE R AIEAA+KA Sbjct: 9 RLKDASLLKSQCYVNGRWVGEGE---IAVTNPATGETLASVPRFGGAEAREAIEAAEKAF 65 Query: 62 PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121 W TAKER+ LRRW++LM+EN++DLA +MT EQGKPL E++GEI YAA+F+E+F E Sbjct: 66 KPWAKKTAKERSKILRRWYELMMENKEDLAFIMTSEQGKPLTESRGEIDYAANFVEFFAE 125 Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181 EAKRIYGDTIP H+ D RI+V KQPIGVT AITPWNFP+AMITRKAGPALAAGCTMV+KP Sbjct: 126 EAKRIYGDTIPSHKADARIVVGKQPIGVTCAITPWNFPAAMITRKAGPALAAGCTMVVKP 185 Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQL 241 A++TP +ALALAELA RAGIP+GVFSV+TG + E+G E+TSNPIV+ +TFTGSTE+G++L Sbjct: 186 ATETPLTALALAELAHRAGIPEGVFSVITGKSSEIGAEMTSNPIVKLITFTGSTEVGKKL 245 Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301 M + A +KKV+LELGGNAPF+VFDDADLDAAV+GA+ SK+RN GQTCVCANR+YVQ GV Sbjct: 246 MEQSASTVKKVALELGGNAPFLVFDDADLDAAVQGAIASKFRNMGQTCVCANRIYVQSGV 305 Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361 Y+AF KL AV KL +G+G + V GPLI+ AV KVEEHI+DA SKGAKVV GGK Sbjct: 306 YEAFAGKLAEAVKKLKVGDGAQEDVQQGPLINEDAVKKVEEHISDATSKGAKVVLGGKRS 365 Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421 LG +FF+PT+L DV +V+++ETFGP+AP+FRF+ E E I ++N T+FGLASYFY+R Sbjct: 366 DLGHSFFQPTVLTDVTPEMVVTREETFGPVAPLFRFETEEEAIELANATQFGLASYFYSR 425 Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481 D+ R +RVAE LEYG+VGIN GLIS EVAPFGG+K SG+GREGS YG+++++E+KY+ +G Sbjct: 426 DIGRCWRVAEALEYGIVGINEGLISTEVAPFGGVKESGIGREGSHYGMDEFVEVKYMLMG 485 Query: 482 GI 483 G+ Sbjct: 486 GL 487 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: 681 Number of extensions: 9 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: 483 Length of database: 489 Length adjustment: 34 Effective length of query: 449 Effective length of database: 455 Effective search space: 204295 Effective search space used: 204295 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