Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate RR42_RS21760 RR42_RS21760 succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__Cup4G11:RR42_RS21760 Length = 482 Score = 221 bits (562), Expect = 6e-62 Identities = 159/474 (33%), Positives = 233/474 (49%), Gaps = 29/474 (6%) Query: 4 KQQLLIDGAWVDGDAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFA 63 +QQ IDG W D T+P +GE + A + A+ AA +A P W R+ Sbjct: 11 RQQCYIDGRWTDAQR-HIDVTNPATGERVGQVPLLGADETRQAIEAANRALPAWRARTAK 69 Query: 64 ERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGER 123 ER A++ ++ E L +++ LA + E GKP EAR E+G A S + G+R Sbjct: 70 ERSALLRKWFELLLANQDDLARIMTAEQGKPFAEARGEIG-----YAASFIEWFAEEGKR 124 Query: 124 A------RDIGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQT 177 + + R V+ P GV A P+NFP + PAL AG +V KP+ QT Sbjct: 125 VYGETIPAPVSNQRIVVTKEPVGVCAAITPWNFPAAMITRKAGPALAAGCTMVVKPASQT 184 Query: 178 PMTADLTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLLHRQF 236 P+TA + AG+PAGV+++V G AA +G L+ + + L FTGS +VG L Q Sbjct: 185 PLTALAMVALAERAGIPAGVLSVVTGSAAAIGGELSSNPLVRKLTFTGSTEVGRTLMAQT 244 Query: 237 GGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGD 296 + K+ ++ELGGN P +V + D +AAV + S + + GQ C CA RL V H V D Sbjct: 245 ASTIKKV-SMELGGNAPFIVFEDADLDAAVEGAIVSKYRNAGQTCVCANRLYV-HSKVYD 302 Query: 297 DLIDALTSAIAELRVAAPFSEP---APFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMR 353 + L +A+ L+V + P G + + + D +++G R L + Sbjct: 303 AFAEKLVAAVRALKVGNGMEDGVRIGPLIDGKAVTKVEEHI----TDAISKGARVLQGGK 358 Query: 354 RLQAGTSLLSPG-LIDVT-GCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLI 411 R G S P L DVT G V EE FGPL + R+ DE +A+ANDT +GL++ Sbjct: 359 RHALGQSFFEPTVLADVTPGMLVAREETFGPLAPLFRFETEDEVVAMANDTEFGLASYFY 418 Query: 412 GGERADWDDFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSAYYAAD 463 + R+ G+V N TG S+ APFGG+ SG R ++Y + Sbjct: 419 ARDLGRVWRVSERLEYGMVGVN---TGLISNEVAPFGGVKQSGVGREGSHYGIE 469 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: 600 Number of extensions: 31 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: 482 Length adjustment: 34 Effective length of query: 455 Effective length of database: 448 Effective search space: 203840 Effective search space used: 203840 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