Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate BWI76_RS00845 BWI76_RS00845 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:Q8U0B6 (330 letters) >FitnessBrowser__Koxy:BWI76_RS00845 Length = 334 Score = 185 bits (470), Expect = 1e-51 Identities = 127/342 (37%), Positives = 183/342 (53%), Gaps = 29/342 (8%) Query: 1 MIKAAVVGASGYIGGELVRLLAMHPEVEITAIT---SRQYAGKKVHKVHPNLRGL----- 52 M+ +VGASGY G ELV + HP + ITA+T AGK V +HP L+G+ Sbjct: 1 MLNTLIVGASGYAGAELVAYVNRHPHMTITALTVSAQSNDAGKLVSDLHPQLKGIVDLPL 60 Query: 53 -DLRFTNDYNFDADVIFLAVPHGTSMKIIEEFLGSAKII-DMSADFRIKK-ELYEKYYG- 108 + ++++ DV+FLA H S + +FL + ++ D+S FR+ YEKYYG Sbjct: 61 QPMSDISEFSAGVDVVFLATAHEVSHDLAPQFLAAGCVVFDLSGAFRVNDGAFYEKYYGF 120 Query: 109 PHEKPELIDRFTYGLPELHRKEIKKAELVANPGCNATATILGLYP-----FKDLTQEAIV 163 H+ PEL+++ YGL E +++K+A L+A PGC TA L L P DL Q ++ Sbjct: 121 THQHPELLEQAVYGLAEWSVEKLKEANLIAVPGCYPTAAQLSLKPLIDAGLLDLNQWPVI 180 Query: 164 DLKVSSSAGGRRENIASIHPERSNVVRVYKPYHHRHEAEVLQETRVKAMFTVHSVDLVRG 223 + S GR+ +I + E S ++ Y ++HRH E+ +FT H + RG Sbjct: 181 NATSGVSGAGRKASIGNSFCEVS--LQPYGVFNHRHHPEISTHLGADVIFTPHLGNFKRG 238 Query: 224 LLATIYFRYE-GNERELLRKLLM--YKDEPFVRIVTDKGGLQRYPDPKYVIGSNFIDIGF 280 +L TI R + G +E + + Y D+P VR+ DKG P K V+G F DIGF Sbjct: 239 ILETITCRLKPGVSKEQVAAVFQQAYADKPLVRLY-DKG----VPALKNVVGLPFCDIGF 293 Query: 281 AYDSENSRVMVFSAIDNLIKGGAGQAVQNMNIMFGLKETTGL 322 A E+ ++V +A DNL+KG A QAVQ NI FG ET L Sbjct: 294 AVQDEH--IIVVAAEDNLLKGAAAQAVQCANIRFGFAETQSL 333 Lambda K H 0.321 0.139 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: 302 Number of extensions: 17 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 Aug 03 2021. The underlying query database was built on Aug 03 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