Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf6N2E2_859 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Query= reanno::WCS417:GFF2159 (526 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_859 Length = 526 Score = 826 bits (2133), Expect = 0.0 Identities = 409/526 (77%), Positives = 462/526 (87%) Query: 1 MTSFLGHNYIGGQRSANGSVTLQSVDATSGEALPQHFYQATPQEVDAAAKAAAQAYPAYR 60 M+ G N+IGGQRSA G++ ++SVDA++GE LP F+QAT QEV+ AA AA A+ +YR Sbjct: 1 MSLITGQNFIGGQRSAAGTIIVKSVDASTGETLPYAFHQATAQEVENAAHAAHHAFSSYR 60 Query: 61 ALSAARRAQFLDAVADELDALGDEFVELVCRETALPAARIKGERGRTSGQMRLFATVLRR 120 LSA++RA+FLDA+A EL+AL DEF+ LVCRETALP ARI+GER RTSGQMRLFA VLRR Sbjct: 61 TLSASKRAEFLDAIAQELEALDDEFIALVCRETALPVARIQGERARTSGQMRLFANVLRR 120 Query: 121 GDFYGARIDKALPDRQPMPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180 GDFYGARID+ALP R+P+PRPDLRQYR +GPVAVFGASNFPLAFSTAGGDTA+ALAAGC Sbjct: 121 GDFYGARIDQALPLRKPLPRPDLRQYRTAIGPVAVFGASNFPLAFSTAGGDTASALAAGC 180 Query: 181 PVVFKAHSGHMATAERVADAIIRAAEATEMPAGVFNMIFGGGVGEALVKHPAIQAVGFTG 240 PVVFKAHSGHMATAE+VA+AIIRAAE + MPAGVFNMI+G GVGEALVKHP I+ VGFTG Sbjct: 181 PVVFKAHSGHMATAEQVANAIIRAAERSGMPAGVFNMIYGSGVGEALVKHPLIKGVGFTG 240 Query: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALKARAESVARDLTASVVQGCGQF 300 SLKGGRALCDMAAARP+PIPVFAEMSSINPV++LP AL RA+S+A DL ASVVQGCGQF Sbjct: 241 SLKGGRALCDMAAARPEPIPVFAEMSSINPVVILPHALSRRADSIAHDLAASVVQGCGQF 300 Query: 301 CTNPGLVIGVASPEFTAFTQQVAQLIGDQPAQTMLNAGTLSSYGKGLEKLLAHPGIQHLA 360 CTNPGLV+G+ S FTAF +VA L+ DQPAQTMLNAGTL SY GL+ L AHPGI HLA Sbjct: 301 CTNPGLVVGIRSDAFTAFQDRVAALMNDQPAQTMLNAGTLRSYAAGLQNLHAHPGIVHLA 360 Query: 361 GSQQAGNQAQPQLFKADVRLLIDGDEVLQEEVFGPTTVFVEVADQAQLSAALHGLHGQLT 420 GS Q +QAQPQLFKADV LL++GD+VLQEE+FGPT++F+EVADQAQLSAA++ L GQLT Sbjct: 361 GSDQQAHQAQPQLFKADVELLLNGDKVLQEEIFGPTSIFIEVADQAQLSAAINALRGQLT 420 Query: 421 ATIIGEPADLQQFAELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480 AT+IGEP DL QF ELT LLE KVGRIL+NGYPTGVEVCDSMVHGGPYPATSD+RGTSVG Sbjct: 421 ATLIGEPEDLTQFTELTALLEMKVGRILINGYPTGVEVCDSMVHGGPYPATSDSRGTSVG 480 Query: 481 TLAIDRFLRPVCFQNYPDSLLPDALKNANPLRIQRLVDGTPSRDPL 526 TLAIDRFLRPVCFQNYPD+LLPDALKNANPL I RLVDG SRD L Sbjct: 481 TLAIDRFLRPVCFQNYPDALLPDALKNANPLNISRLVDGCLSRDRL 526 Lambda K H 0.319 0.135 0.392 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: 901 Number of extensions: 25 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