Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.-; EC 1.2.1.103 (characterized, see rationale)
to candidate AZOBR_RS07795 AZOBR_RS07795 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:Q5JFW1 (330 letters) >FitnessBrowser__azobra:AZOBR_RS07795 Length = 350 Score = 230 bits (586), Expect = 4e-65 Identities = 147/349 (42%), Positives = 199/349 (57%), Gaps = 27/349 (7%) Query: 2 IKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRGLDL----RFT 57 I+ ++GASGY G ELVR+L HP VEI A+T+ R AG+ + +V P+L +L + Sbjct: 8 IRVGILGASGYTGAELVRMLLRHPGVEICALTAERQAGKPMAEVFPHLGQFNLPGLVKIE 67 Query: 58 NTKEFDADVIFLAVPHGTSMEIIDDYLGSAKIIDMSADFRLREDL-YREYYG-EHKRPEL 115 D +F A+PHGT+ E+I K++D+SADFRL + Y +YG EH+ EL Sbjct: 68 EVAWDKLDAVFCALPHGTTQEVIAGLPRHIKVVDLSADFRLSDPAEYATWYGHEHRAVEL 127 Query: 116 IEEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFRELTDEAI------VDLKVSS 169 +E YGL E +R+ +RKA +VANPGC T ++LAL P L DE I +D K Sbjct: 128 QKEVAYGLTEFNRQGVRKARVVANPGCYPTCSLLALLPL--LMDEMIEPGGIVIDAKSGV 185 Query: 170 SAGGRRENVASIHPERSHVVRVYKPYHHRHEGEVIQETGVKA------AFTVHSVDIIRG 223 S GR ++ E S Y HHRH E+ QE + A +FT H V + RG Sbjct: 186 SGAGRDAKQQNLFTEVSEGFNAYGVGHHRHMPEIEQELRLAAGRPVTVSFTPHLVPMNRG 245 Query: 224 LLATIYFRF-EGSTRELLRKLLV--YKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGF 280 ++ATIY R +G T + LR L Y+ EPFV + G+ P ++V SN A IG Sbjct: 246 MMATIYVRMADGVTADDLRATLTARYESEPFVNVTA--AGIA--PATRHVRASNQALIGV 301 Query: 281 AHDEENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVYP 329 D AI++S IDNL+KG SGQA+QNMN+MFGL E TGL P++P Sbjct: 302 FPDRTPRGAIIVSVIDNLVKGASGQAIQNMNVMFGLGETTGLEQAPLFP 350 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: 292 Number of extensions: 16 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: 350 Length adjustment: 28 Effective length of query: 302 Effective length of database: 322 Effective search space: 97244 Effective search space used: 97244 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