Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298 Length = 481 Score = 916 bits (2367), Expect = 0.0 Identities = 458/481 (95%), Positives = 474/481 (98%) Query: 1 MSQAQRFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWS 60 ++ ++RFDNYINGQWVAGADYC N+NPS+LSDVIGEYAKAD QVNAAI+AARAAFPAWS Sbjct: 1 VADSKRFDNYINGQWVAGADYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPAWS 60 Query: 61 TSGIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120 TSGIQARHDALDKVGSEILARREELG LLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR Sbjct: 61 TSGIQARHDALDKVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120 Query: 121 LSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELV 180 LSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELV Sbjct: 121 LSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELV 180 Query: 181 PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSC 240 PGCAWALAEIISRAGFPAG FNLVMGSGRVVGD+LVNSPKVDGISFTGSVGVGRQIAV+C Sbjct: 181 PGCAWALAEIISRAGFPAGAFNLVMGSGRVVGDILVNSPKVDGISFTGSVGVGRQIAVNC 240 Query: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQF 300 VSRQAKVQLEMGGKNPQIILDDADLKQAVEL+VQSAFYSTGQRCTASSRLIVTAGIHD+F Sbjct: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTAGIHDKF 300 Query: 301 VAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDT 360 VAAMAERM+SIKVGHALK+GTDIGPVVS+AQL QDLKYIDIGQSEGARLVSGGGLVTCDT Sbjct: 301 VAAMAERMQSIKVGHALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGGLVTCDT 360 Query: 361 EGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL 420 EGY+LAPTLFADSEA+MRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL Sbjct: 361 EGYFLAPTLFADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL 420 Query: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG Sbjct: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480 Query: 481 S 481 S Sbjct: 481 S 481 Lambda K H 0.318 0.134 0.390 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: 876 Number of extensions: 21 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: 481 Length of database: 481 Length adjustment: 34 Effective length of query: 447 Effective length of database: 447 Effective search space: 199809 Effective search space used: 199809 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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