Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_086510804.1 BZY95_RS15485 NAD-dependent succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >NCBI__GCF_002151265.1:WP_086510804.1 Length = 481 Score = 215 bits (547), Expect = 3e-60 Identities = 157/460 (34%), Positives = 230/460 (50%), Gaps = 10/460 (2%) Query: 9 IDGAWVDGDAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFAERQAV 68 I G W D + RF T+P +GETL + SA AVAAA A+P W R++ +R A+ Sbjct: 14 IGGQWRDAER-RFDVTNPANGETLASVPDLSADDARDAVAAAEAAWPAWRRQTAKQRAAL 72 Query: 69 VERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGERARDIG 128 + + + + H+E LA + E GKPL E+R EV V GE G Sbjct: 73 LRAWFDAIMAHQESLARMMTLEQGKPLAESRGEVAYGASFVEFYAEQAKRMAGETLPSHG 132 Query: 129 -DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTADLTLQC 187 D R ++ P GV+A P+NFP + PAL AG VV KP+E TP+TA + Sbjct: 133 ADKRILVFREPVGVVAAITPWNFPLAMITRKCAPALAAGCPVVIKPAEATPLTALALARL 192 Query: 188 WLEAGLPAGVINLVQGA--AEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVDKILA 245 + G PAGV+N+V + AE+G+ L + + FTGS VG L Q G V K + Sbjct: 193 AEQVGFPAGVLNVVTASRPAEIGEVLTSDPRVRKVSFTGSTAVGKRLLAQCAGTVKK-AS 251 Query: 246 LELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDALTSA 305 +ELGGN P +V D D +AAV + S + + GQ C C RL+V G V + ++ L + Sbjct: 252 MELGGNAPFIVFDDADLDAAVEGAVASKYRNSGQTCVCTNRLLVQSG-VYEAFVEKLAAR 310 Query: 306 IAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQAGTSLLSPG 365 +A+L+V E L + A D + + D +A+G R + G + P Sbjct: 311 VAQLKVGNGLDE-GVVQGPLINQAAVDKVQSHIADALAKGARLVCGGEPHALGGTFFQPT 369 Query: 366 LI-DVTG-CDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGERADWDDFLL 423 ++ DVT V EE FGPL V R+ ++AIA+AN T +GL+A + + Sbjct: 370 VVADVTDEMRVAREETFGPLAPVFRFDSDEQAIAMANATEFGLAAYFYARDYRRIWHVME 429 Query: 424 RIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463 + G+V N ++ APFGG+ +SG R +++ D Sbjct: 430 GLEYGMVAVNEGIL-STELAPFGGVKESGLGREGSHHGLD 468 Lambda K H 0.319 0.135 0.409 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: 634 Number of extensions: 38 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: 489 Length of database: 481 Length adjustment: 34 Effective length of query: 455 Effective length of database: 447 Effective search space: 203385 Effective search space used: 203385 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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