Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate PP_2585 PP_2585 Alpha-ketoglutaric semialdehyde dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_612 (526 letters) >FitnessBrowser__Putida:PP_2585 Length = 526 Score = 779 bits (2011), Expect = 0.0 Identities = 394/519 (75%), Positives = 434/519 (83%) Query: 8 NYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYRSLSAVRR 67 N+I G S G L S+DA TGE LP+ F QAT +EV+AAA+AA AYP+YRS +R Sbjct: 8 NHIAGQLSGHGDVLLHSLDAHTGETLPYAFHQATGDEVEAAAQAAEVAYPSYRSTRPDQR 67 Query: 68 AEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRRGDFYGAR 127 A FL+AIA ELDALGD+F+ V RETALP ARI+GER RTS Q+RLFA+V+RRGDFY AR Sbjct: 68 AAFLDAIASELDALGDDFIQDVMRETALPEARIRGERSRTSNQLRLFAEVVRRGDFYAAR 127 Query: 128 IDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGCPVVFKAH 187 IDRALP+RTPLPRPDLRQYRIG+GPVAVFGASNFPLAFSTAGGDTASALAAGCPVVFKAH Sbjct: 128 IDRALPQRTPLPRPDLRQYRIGVGPVAVFGASNFPLAFSTAGGDTASALAAGCPVVFKAH 187 Query: 188 SGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGGVGEWLVKHPAIQAVGFTGSLKGGRA 247 SGHM TA HVA AI RA + MPAGVFNMIYG GVGE LVKHPAIQAVGFTGSL+GGRA Sbjct: 188 SGHMLTAAHVAAAIDRAVTGSGMPAGVFNMIYGAGVGEALVKHPAIQAVGFTGSLRGGRA 247 Query: 248 LCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQFCTNPGLV 307 LCDMAAARPQPIPVFAEMSSINPV+VLPQAL+ R E VA +L ASVV GCGQFCTNPGLV Sbjct: 248 LCDMAAARPQPIPVFAEMSSINPVVVLPQALQARGEQVATELAASVVLGCGQFCTNPGLV 307 Query: 308 IGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLAGRQQQGN 367 +GIRSP F F Q + A + DQ PQTMLNAGTL+SY +Q LLAHPGI+HLAG+ Q GN Sbjct: 308 VGIRSPHFEHFLQTLVARMADQGPQTMLNAGTLRSYQNAVQHLLAHPGIQHLAGQPQTGN 367 Query: 368 QAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLTATMIGEP 427 QAQPQLFKAD SLL+NGD LQEEVFGP TV VEVAD QL AL L GQLTAT+I EP Sbjct: 368 QAQPQLFKADVSLLLNGDPLLQEEVFGPCTVVVEVADAQQLAEALRHLQGQLTATLIAEP 427 Query: 428 ADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVGTLAIDRF 487 D F+ L PLLE+K GR+LLNGYPTGVEV D+MVHGGPYPATSDARGTSVGTLAIDRF Sbjct: 428 DDLRTFASLVPLLERKAGRLLLNGYPTGVEVSDAMVHGGPYPATSDARGTSVGTLAIDRF 487 Query: 488 LRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL 526 LRPVCFQNYPD+LLP+ LKNANPLGI RL++GV REA+ Sbjct: 488 LRPVCFQNYPDALLPDALKNANPLGIARLLEGVSSREAV 526 Lambda K H 0.319 0.135 0.395 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: 980 Number of extensions: 33 Number of successful extensions: 1 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: 526 Length of database: 526 Length adjustment: 35 Effective length of query: 491 Effective length of database: 491 Effective search space: 241081 Effective search space used: 241081 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