Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Pf1N1B4_4355 Gamma-glutamyl-aminobutyraldehyde dehydrogenase (EC 1.2.1.-)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4355 Length = 496 Score = 196 bits (498), Expect = 2e-54 Identities = 152/470 (32%), Positives = 234/470 (49%), Gaps = 20/470 (4%) Query: 5 FIDGAWVDG-AGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAA--WSALDLDA 61 FIDG + +G F +P + AS D AV ARR F + W+ L Sbjct: 22 FIDGQYCPALSGDTFECISPVDGRFLANIASTDEADANAAVQVARRTFESGIWAKLPPAE 81 Query: 62 RCTIVKRFAALLVERKEALATMIGRETGKPLWEART-EVASMAAKVDISITAYHERTGEK 120 R ++ RFA L+++ +E LA + + GKP+ ++ + ++ + A + S A + E Sbjct: 82 RKRVLIRFADLILQNQEELALLETLDMGKPISDSMSIDIPATANAIRWSAEAIDKIYDEV 141 Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 A D + ++ P GVVA P+NFP + + PAL AGN+ + KPSE +P A Sbjct: 142 AATPHDQLGLITREPAGVVAAIVPWNFPLIMASWKFAPALAAGNSFILKPSEKSPLTAIR 201 Query: 181 TVEIWRDAGLPAGVLNLVQGEKDT-GVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 ++ +AG+P GV N++ G T G ALA H +D L FTGS+ L G Sbjct: 202 IAQLALEAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFTGSTAIAKQLLIYAGQSNMK 261 Query: 240 VLALEMGGNNPLVV-AEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298 + LE GG +P VV A+ D+ AA A+ + + G+ CT R+LV R + ++F+ Sbjct: 262 RVWLEAGGKSPNVVFADAPDLRAAARAAVSAIAFNQGEVCTAGSRLLVER-SIREQFIPL 320 Query: 299 LADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLG---ASPIIEMKQR--- 352 L + A + DP+ +GAV+ R ++ R + +G + +I R Sbjct: 321 LVE-ALQAWKPGHALDPETTVGAVVDQRQLDNVL----RYIQVGKDQGAQLIAGGNRTLA 375 Query: 353 DPALGFVNAAILD-VTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLAD 411 D +V AI D VTN + EE FGP+ ++ + ++A+ AND+ FGL+AG+ Sbjct: 376 DTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALQIANDSIFGLAAGVWTS 435 Query: 412 DEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461 + HTF R +RAG V W +G APFGG +SGN R + +A D Sbjct: 436 NLSKAHTFARGLRAGSV-WVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFD 484 Lambda K H 0.320 0.134 0.402 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: 535 Number of extensions: 31 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: 487 Length of database: 496 Length adjustment: 34 Effective length of query: 453 Effective length of database: 462 Effective search space: 209286 Effective search space used: 209286 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