Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 215 bits (548), Expect = 2e-60 Identities = 152/463 (32%), Positives = 226/463 (48%), Gaps = 9/463 (1%) Query: 13 TQFIAGQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTER 72 + +I G+W G+ F VNPA+ EVI Q + A AI +A+ A WS S ER Sbjct: 13 SSYIDGRWTVGE-QRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANER 71 Query: 73 LVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAERTG-TVE 131 ++ + + EH E R + LE GK L E++ E+ I + G T+ Sbjct: 72 AALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGDTIP 131 Query: 132 NPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELT 191 P + + +P GVVA P+NFP + AL AG T + +PS LTP A Sbjct: 132 APANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAM 191 Query: 192 MQLWQQAGLPNGVLNLLQGE--IATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGK 249 +L ++AG+P GV N++ GE + GK L H + FTGS+ G +L Q A K Sbjct: 192 AELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKK 251 Query: 250 ILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKL 309 + ++E+GGN P I+ + A++DAAV + S + ++GQ C C R+F+ K A K Sbjct: 252 V-SMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGV-AAAFTEKF 309 Query: 310 LTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLGFV 369 + A + LGD + G MIS A ++K D A+G + G F+ Sbjct: 310 TAAVANLKLGDGLGDGVT-VGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGESFL 368 Query: 370 TPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSETDYQH 428 P I+ DVT+ PLA E FGP+ + + A+ AN+T +GL+A A Sbjct: 369 APVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGRIFR 428 Query: 429 FYRRIRAGIVNWNKPITGASSAAPFGGIGASGNHRASAYYAAD 471 + G+V N+ I +++AAPFGG+ SGN R + Y D Sbjct: 429 VAEGLEYGMVGVNEGII-SNAAAPFGGVKQSGNGREGSKYGLD 470 Lambda K H 0.317 0.133 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: 511 Number of extensions: 29 Number of successful extensions: 6 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: 498 Length of database: 485 Length adjustment: 34 Effective length of query: 464 Effective length of database: 451 Effective search space: 209264 Effective search space used: 209264 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