Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate PfGW456L13_3604 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604 Length = 490 Score = 194 bits (493), Expect = 6e-54 Identities = 152/461 (32%), Positives = 230/461 (49%), Gaps = 17/461 (3%) Query: 4 KQQLLIDGAWVDGDAARFAKT-DPVSGETLWTATAASATQVEHAVAAARQAFPD-WARRS 61 + QL I+G WV D + DP + + A + V+HAV AAR+AF + W + S Sbjct: 2 RDQLYINGEWVSPDLGGYLDVIDPATEQAFHRVAAGTEEDVDHAVRAARRAFDNGWGQTS 61 Query: 62 FAERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIG--KVAISITAYHER 119 AER +E + LE+ ++ LA ++ GKPL EA+ ++G I + + ++ Sbjct: 62 GAERGQWLEALADELESGQQALAELEVRDNGKPLPEAQWDIGDAIACFRYYAGLARELDQ 121 Query: 120 TGERARDIGDARAV--LRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQT 177 ++ + DAR +RH P GV P+N+P + + PAL AG VV KPSE T Sbjct: 122 QQDQPLALPDARFCCRIRHEPIGVAGQIIPWNYPLLMAAWKVAPALAAGATVVLKPSELT 181 Query: 178 PMTADLTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLLHRQF 236 P+TA GLPAGV+NLV G A+ G L +D L FTGS G + Sbjct: 182 PLTALELAAAADRIGLPAGVLNLVTGLGADAGSPLTEHPGVDKLAFTGSVPTGAKIMSAA 241 Query: 237 GGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGD 296 + K ++LELGG + +V D D EAAV IL F + GQ C+ RL+V + Sbjct: 242 ARDI-KNISLELGGKSAFIVFDDADVEAAVEWILFGIFWNQGQVCSATSRLLVQE-TIAA 299 Query: 297 DLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRR-- 354 LI+ L ++ + P +P L S D +L D +A G R L+ RR Sbjct: 300 RLIERLVEETRKISI-GPGMQPGVLLGPLVSQGQYDKVLGFIDQGLASGARLLTGGRRPA 358 Query: 355 -LQAGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLI 411 L+ G + P + D G + EE FGP+L + R++ ++A+ +AN +R+GL+A ++ Sbjct: 359 HLREG-YFVEPAIFDEPGHSSILWREEVFGPVLCIKRFKTEEQALQMANASRFGLAAAVM 417 Query: 412 GGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSG 452 + ++RAGIV W + +AP+GG+ SG Sbjct: 418 SADLQRTARVANQLRAGIV-WVNCSQPTFVEAPWGGMKHSG 457 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: 639 Number of extensions: 30 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: 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