Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 216 bits (549), Expect = 2e-60 Identities = 158/447 (35%), Positives = 222/447 (49%), Gaps = 17/447 (3%) Query: 14 VDGDAARFAKT----DPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFAERQAVV 69 VDG A+T DP +G A AS ++ AVAAAR+AFP WA +R A + Sbjct: 8 VDGKPLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAI 67 Query: 70 ERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVA-ISITAYHERTGERARDIG 128 + +E ++ LA ++ E GKP+ A VG ++G +A TA + +D Sbjct: 68 LAIADSIEAAKDELARLLSAEQGKPVPNA---VGEIMGALAWARATAGLRPAVDVLKDDD 124 Query: 129 DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTADLTLQCW 188 R + +P GV+A P+NFP + HI+P L+AGN VV KPS TP+ A L + Sbjct: 125 SVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAA-LRMVEI 183 Query: 189 LEAGLPAGVINLVQGAAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVDKILALEL 248 A LP GV+N V G E+G+A+A ID ++FTGS G + G K L LEL Sbjct: 184 ANAHLPPGVLNSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMAD-GAANLKRLTLEL 242 Query: 249 GGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDALTSAIAE 308 GGN+ +V D + I AF + GQ C +R+ V H ++ D L + L + +A Sbjct: 243 GGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYV-HESIHDALAEKL-AEMAR 300 Query: 309 LRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQAGTSLLSP--GL 366 V P S+ A + + + + D + A DD A GGR L+ + G P + Sbjct: 301 TAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAG-GEAREGDGYFFPLSVV 359 Query: 367 IDVT-GCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGERADWDDFLLRI 425 +DVT G + DEE FGP+L V RY D ++A+A AN GL + + A F R+ Sbjct: 360 VDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRL 419 Query: 426 RAGIVNWNRQTTGASSDAPFGGIGDSG 452 AG V W S D PFGG SG Sbjct: 420 EAGTV-WVNDHASISPDVPFGGAKQSG 445 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: 677 Number of extensions: 42 Number of successful extensions: 7 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: 469 Length adjustment: 34 Effective length of query: 455 Effective length of database: 435 Effective search space: 197925 Effective search space used: 197925 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: 51 (24.3 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