Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__BFirm:BPHYT_RS30285 Length = 490 Score = 220 bits (561), Expect = 8e-62 Identities = 166/477 (34%), Positives = 235/477 (49%), Gaps = 29/477 (6%) Query: 4 KQQLLIDGAWVDG-DAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62 + Q LIDGAW D ARFA T+P +GET+ + A A AA +AFP W Sbjct: 12 RPQNLIDGAWTGAADGARFAVTNPATGETIVEVADSGAADARAATDAAARAFPAWRDTLP 71 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122 ER ++ R+ + + + LA ++ E GKPL EAR G+VA + E Sbjct: 72 RERAEILRRWHALIVANTDDLAKLMSMEQGKPLAEAR-------GEVAYGASYVAWFADE 124 Query: 123 RARDIGD--------ARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPS 174 R GD R P GV+A P+NFP + I PAL AG VV KP+ Sbjct: 125 ATRIYGDLIPQQQRGKRMSAVKEPVGVIAAITPWNFPLAMIARKIAPALAAGCTVVAKPA 184 Query: 175 EQTPMTADLTLQCWLEAGLPAGVINLV-----QGAAEVGQALAGSADIDGLLFTGSAKVG 229 E TP+TA EAGLP GV+N++ QG A V LA S + + FTGS VG Sbjct: 185 EDTPLTALALAVLAQEAGLPDGVLNMLSASREQGIAAVADWLADSR-VRKITFTGSTPVG 243 Query: 230 GLLHRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIV 289 L R+ G + K L+LELGGN P +V D D +AAV ++ + F +GGQ C C R+ V Sbjct: 244 KHLARESAGTLKK-LSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYV 302 Query: 290 PHGAVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPL 349 G V + D L + L+V AP ++P + + A + +D V G + L Sbjct: 303 QAG-VYERFADLLAKRVGALKV-APATDPQAQIGPMINERAIQKIARHVEDAVKHGAKVL 360 Query: 350 SRMRRL-QAGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGL 406 +RL + G + +P ++ D V EE FGP+ + R+ + EAI L+NDT +GL Sbjct: 361 VGGKRLTELGPNYYAPTVLTDARDDMLVSCEETFGPVAPLFRFNEEAEAIRLSNDTPFGL 420 Query: 407 SAGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463 +A + + ++ AG++ N +S APFGG+ +SG R + Y D Sbjct: 421 AAYFYTQDVRRINRVAAQLEAGVIGINEGAV-SSEAAPFGGVKESGYGREGSKYGLD 476 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: 650 Number of extensions: 45 Number of successful extensions: 5 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: 490 Length adjustment: 34 Effective length of query: 455 Effective length of database: 456 Effective search space: 207480 Effective search space used: 207480 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 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