Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_043743989.1 AMB_RS09075 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::Q5JFW1 (330 letters) >NCBI__GCF_000009985.1:WP_043743989.1 Length = 346 Score = 229 bits (584), Expect = 8e-65 Identities = 143/349 (40%), Positives = 197/349 (56%), Gaps = 27/349 (7%) Query: 2 IKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRGLDL----RFT 57 + A++GASGY G ELVRLLA+HP +I +T R AGQ + V P+L GL+L Sbjct: 4 VSIAILGASGYTGAELVRLLALHPTFKIKVMTGDRKAGQSMESVFPHLGGLELPTLVAID 63 Query: 58 NTKEFDADVIFLAVPHGTSMEIIDDYLGSAKIIDMSADFRLRE-DLYREYYG-EHKRPEL 115 D +F +PHGT+ E+I S K++D+SADFRL + D Y ++YG EH+ PEL Sbjct: 64 QVDFTTVDAVFCCLPHGTTQEVIAALPASVKVVDLSADFRLFDVDTYAQWYGHEHRAPEL 123 Query: 116 IEEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFREL----TDEAIVDLKVSSSA 171 ++ VYGL EL R + KA LVANPGC T+ L L P + + ++D K S Sbjct: 124 QKQAVYGLTELARDAVAKARLVANPGCYPTSVQLPLIPLLKAGLIEAADIVIDAKSGVSG 183 Query: 172 GGRRENVASIHPERSHVVRVYKPYHHRHEGEVIQETGVKAA--------FTVHSVDIIRG 223 GR A+++ E + + Y HRH E+ E G+ AA FT H + + RG Sbjct: 184 AGRAAKEANLYTEVTEGMHAYGVASHRHAPEI--EQGLSAAAGVPVLVSFTPHLIPMSRG 241 Query: 224 LLATIYFRFEGSTREL-LRKLL--VYKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGF 280 +L+TIY + +G + LR L + EPFVR+V + G+ P ++V GSN I Sbjct: 242 MLSTIYVKTKGGAKAADLRAQLSKTFGGEPFVRVVPE--GV--VPHTRHVRGSNHCLINV 297 Query: 281 AHDEENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVYP 329 D + I+ S IDNL+KG SGQA+QNMNLMFGL E T L P++P Sbjct: 298 FDDRVPGKVIITSVIDNLVKGASGQALQNMNLMFGLPETTALAQQPMFP 346 Lambda K H 0.321 0.140 0.404 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: 306 Number of extensions: 13 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: 330 Length of database: 346 Length adjustment: 28 Effective length of query: 302 Effective length of database: 318 Effective search space: 96036 Effective search space used: 96036 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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