Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein
Query= curated2:B0T8I8 (484 letters) >NCBI__GCF_001906585.1:WP_073948994.1 Length = 462 Score = 198 bits (503), Expect = 4e-55 Identities = 163/455 (35%), Positives = 218/455 (47%), Gaps = 30/455 (6%) Query: 4 GLFIDGVWRAGAGAQATSVDPTTGEVIWRQATASTAE-VAAAVEAARKAFPAWADRSREE 62 G++IDG WR AG A V E + A TAE V AAV AAR A P WA E Sbjct: 6 GMYIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAE 65 Query: 63 RIAVLRRYKDVLVARTGTFAEALSRETGKALWETKAELGSMAGKVEASIKAYDERTGEHA 122 R A L +DVLVAR AE ++ E G L ++A AG A +Y + +A Sbjct: 66 RAARLTALRDVLVARKDEIAETVTAELGSPLAFSQAV---HAGVPIAVAGSYADLAATYA 122 Query: 123 NDMAFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLL 182 + G + + H GV+ + P+N+P H PAL AG T+V KP+E+TPL QL Sbjct: 123 FEEKVGNSTVHHEPVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPLTAQLF 182 Query: 183 VEALEEAGVPAGVINLVQG-GREVGQALIDQ-EIDGLLFTGSAAAGAFFRRHFADRPDVI 240 EA EAG+PAGV+NLV G G GQAL + ++D + FTGS A G RR A + Sbjct: 183 AEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVG---RRIGATAGAAV 239 Query: 241 --LALELGGNNPLVVWDAGDPEAVAALIVQSAFITTGQRCSCARRLIVSDDAAGRAV-ID 297 +ALELGG + V+ + D + V + +GQ CS R++V D AV + Sbjct: 240 KRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVELA 299 Query: 298 AVAALSERLVIGP-WNGGQEPFMGPLISDRAA--AMALAGAKAMPGQTLRAMTSVDGLSR 354 A AA IGP N Q + I A A +AG P + Sbjct: 300 ATAAAKYGDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPCE-----------KG 348 Query: 355 AFVSPGL-VDVTGE-TVPDEELFAPLLQVRRVGSFEEAIAAANATRYGLSAGLVSNETAH 412 FVSP + DVT + TV EE+F P+L + R ++A+ AN T YGL+ + + + Sbjct: 349 YFVSPTVFADVTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAADETE 408 Query: 413 WDRFLTRIRAGVVNWNRPTTGAAGTMPFGGLGNSG 447 F R+ G V+ N PFGG SG Sbjct: 409 AVAFARRMDTGQVDINGGRFNPLA--PFGGYKQSG 441 Lambda K H 0.318 0.134 0.395 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: 546 Number of extensions: 30 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: 484 Length of database: 462 Length adjustment: 33 Effective length of query: 451 Effective length of database: 429 Effective search space: 193479 Effective search space used: 193479 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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