Align 2-ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AO353_14870 AO353_14870 ketoglutarate semialdehyde dehydrogenase
Query= metacyc::MONOMER-18709 (527 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14870 Length = 529 Score = 788 bits (2036), Expect = 0.0 Identities = 401/523 (76%), Positives = 450/523 (86%) Query: 1 MTAILGHNFIGGARSAAGTLFLQSLDAASGEALPYRFVQATPEEVDAAAEAAASAYPHYR 60 M+AI+GHNFIG RSAAG L S+DA SGE LPY F QA+ EE+D AA AA+AYP YR Sbjct: 1 MSAIIGHNFIGFGRSAAGDHVLHSVDAHSGEPLPYDFSQASAEEIDNAAHFAATAYPIYR 60 Query: 61 QLPASRRAEFLDTIAAELDALDDDFVAIVCRETALPATRIQGERSRTSGQLRLFAEVLRR 120 LPA+ RA FL+TIA E+DAL DDF+AIVCRETALPA RIQGER+RTSGQLRLFA VLR+ Sbjct: 61 NLPATVRAGFLETIAEEIDALGDDFIAIVCRETALPAARIQGERARTSGQLRLFARVLRQ 120 Query: 121 GDFHGARIDRARPERKPLPRVDLRQCRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180 GDF GARIDRA PER+P PR D+RQ RIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC Sbjct: 121 GDFLGARIDRALPERQPFPRPDVRQWRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180 Query: 181 PVVFKAHSGHMATAERVAAAILRAAERTGMPAGVFNMIYGGGVGERLVRHPAIQAVGFTG 240 PVVFKAHSGHMATAE VAAAI+RAA+R+GMP GVFNMIYG GVGE LV+HPAIQAVGFTG Sbjct: 181 PVVFKAHSGHMATAELVAAAIIRAAQRSGMPEGVFNMIYGAGVGEALVKHPAIQAVGFTG 240 Query: 241 SLKGGRALCDMAAARAQPIPVFAEMSSINPVVLLPAALKKRGEAVADELSASVVLGCGQF 300 SLKGGRALCDMAAAR QPIPVFAEMSSINPV+LLPAAL R ++A ELSAS+VLG GQF Sbjct: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVLLLPAALAARSASIASELSASIVLGGGQF 300 Query: 301 CTNPGLVIGIRSAQFSAFLERFAARMDDQPAQTMLNTGTLASYEKGLAALHAHPRVRHLA 360 CTNPGL+IG+RSA FSAF+E+ A+++++P QT+LN+GT SYE G+ L HPRV L+ Sbjct: 301 CTNPGLIIGLRSAAFSAFIEQLTAQINEKPPQTLLNSGTRRSYESGVQRLLEHPRVTRLS 360 Query: 361 GQPQEGRQARPQLFQADVSLLLEGDELLQEEVFGPASVVVEVADHAELKRALHGLHGQLT 420 G G Q +PQLF+ADVSLLLEGDE+LQEEVFGPAS+V+EVAD EL+ AL LHGQLT Sbjct: 361 GNLVPGNQVQPQLFKADVSLLLEGDEVLQEEVFGPASIVLEVADERELRLALCALHGQLT 420 Query: 421 ATLIAEAEDLASFADLVPLLEQKAGRLLLNGYPTGVEVCDAMVHGGPYPATSDARGTSVG 480 ATLIAE +DL A L+P+LEQKAGRLLLNGYPTGVEVCDAMVHGGPYPATSDARGTSVG Sbjct: 421 ATLIAEPQDLVLCAQLIPILEQKAGRLLLNGYPTGVEVCDAMVHGGPYPATSDARGTSVG 480 Query: 481 TLAIDRFLRPVCYQNYPDAWLPEALKDGNPLGIARLVDGIVTR 523 +LAI+RFLRPVCYQN PD LP+ALK+ NPLGI RLVDG+ TR Sbjct: 481 SLAIERFLRPVCYQNCPDRLLPDALKNANPLGILRLVDGVNTR 523 Lambda K H 0.321 0.136 0.397 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: 864 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: 527 Length of database: 529 Length adjustment: 35 Effective length of query: 492 Effective length of database: 494 Effective search space: 243048 Effective search space used: 243048 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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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