Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate BWI76_RS00845 BWI76_RS00845 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::Q5JFW1 (330 letters) >FitnessBrowser__Koxy:BWI76_RS00845 Length = 334 Score = 179 bits (454), Expect = 9e-50 Identities = 129/345 (37%), Positives = 193/345 (55%), Gaps = 35/345 (10%) Query: 1 MIKAAVVGASGYIGGELVRLLAMHPEVEITAIT---SRRFAGQKVHKVHPNLRGL-DLRF 56 M+ +VGASGY G ELV + HP + ITA+T AG+ V +HP L+G+ DL Sbjct: 1 MLNTLIVGASGYAGAELVAYVNRHPHMTITALTVSAQSNDAGKLVSDLHPQLKGIVDLPL 60 Query: 57 ---TNTKEFDA--DVIFLAVPHGTSMEIIDDYLGSAKII-DMSADFRLRED-LYREYYG- 108 ++ EF A DV+FLA H S ++ +L + ++ D+S FR+ + Y +YYG Sbjct: 61 QPMSDISEFSAGVDVVFLATAHEVSHDLAPQFLAAGCVVFDLSGAFRVNDGAFYEKYYGF 120 Query: 109 EHKRPELIEEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFRELTDEAIVDLK-- 166 H+ PEL+E+ VYGL E +++++A L+A PGC TA L+L P L D ++DL Sbjct: 121 THQHPELLEQAVYGLAEWSVEKLKEANLIAVPGCYPTAAQLSLKP---LIDAGLLDLNQW 177 Query: 167 --VSSSAG----GRRENVASIHPERSHVVRVYKPYHHRHEGEVIQETGVKAAFTVHSVDI 220 +++++G GR+ ++ + E S ++ Y ++HRH E+ G FT H + Sbjct: 178 PVINATSGVSGAGRKASIGNSFCEVS--LQPYGVFNHRHHPEISTHLGADVIFTPHLGNF 235 Query: 221 IRGLLATIYFRFE-GSTRELLRKLL--VYKDEPFVRLVTDKGGLQRFPDPKYVIGSNFAD 277 RG+L TI R + G ++E + + Y D+P VRL DKG P K V+G F D Sbjct: 236 KRGILETITCRLKPGVSKEQVAAVFQQAYADKPLVRLY-DKG----VPALKNVVGLPFCD 290 Query: 278 IGFAHDEENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGL 322 IGFA +E+ IV++A DNL+KG + QAVQ N+ FG E L Sbjct: 291 IGFAVQDEH--IIVVAAEDNLLKGAAAQAVQCANIRFGFAETQSL 333 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: 283 Number of extensions: 9 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: 330 Length of database: 334 Length adjustment: 28 Effective length of query: 302 Effective length of database: 306 Effective search space: 92412 Effective search space used: 92412 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