Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate WP_091368988.1 BLU33_RS02870 aldehyde dehydrogenase (NADP(+))
Query= metacyc::G1G01-1343-MONOMER (525 letters) >NCBI__GCF_900105165.1:WP_091368988.1 Length = 527 Score = 461 bits (1185), Expect = e-134 Identities = 254/517 (49%), Positives = 324/517 (62%), Gaps = 2/517 (0%) Query: 3 LTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETS 62 + GN +I A DP+TG+ L + + + A AAF Y+ T Sbjct: 2 INGNNIIACNYTEIEGQAFTVADPSTGEKLSGEFYEADTLIIDKTLNAATAAFKVYKNTM 61 Query: 63 LEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGEW 122 +A+FL AIA +I ALGD LI+RAV E+GLP RI GE GRT QLR FA V G W Sbjct: 62 PATKAKFLRAIANEIAALGDVLINRAVAESGLPVGRIIGEMGRTTGQLRMFADMVEEGSW 121 Query: 123 LDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPVV 182 +D ID+A +R P+PR+D+R+ A+GPV VFGASNFPLAFSVAGGDTASALAAGCPV+ Sbjct: 122 VDAVIDTAQLDRVPIPRSDIRRMLTAIGPVVVFGASNFPLAFSVAGGDTASALAAGCPVI 181 Query: 183 VKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGS 242 VK H AHPGTS LVG A+++A K+ G+P+GVFSLL+ SG VG ALV + KAV FTGS Sbjct: 182 VKVHPAHPGTSALVGAAISKAAKETGMPDGVFSLLFDSGYTVGAALVKHEQTKAVAFTGS 241 Query: 243 RSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFC 302 GGMAL + AQ R IPV+ EM SINPV L L A+ E L + S+T GAGQFC Sbjct: 242 YKGGMALIKLAQERKSLIPVFTEMGSINPVVLLPGILDAQPEVLVAKYAGSITLGAGQFC 301 Query: 303 TNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAY-QAGIAALADNPHAQAIT 361 TNPGL++A + L RFITA G ++ + TMLTPGI+ Y LA+N Sbjct: 302 TNPGLILAIRSAGLDRFITALGGAIELVPSATMLTPGIWKNYGTLAEETLAENGIELIAK 361 Query: 362 SGQAG-QGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420 S + NQ A + A+ F+A+ E+FG SL+V D ++ QV L+GQ Sbjct: 362 SKLINTEKVNQSVATVATVSAKNFIANKKFSEEIFGPWSLLVVADDIAELEQVIASLDGQ 421 Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480 LT T+ + ++ ++L L +GR+++NG PTGVEVC AM HGGPFP+TSD+R TS Sbjct: 422 LTTTVMAQKEELPQYTSVLNALTEISGRVILNGVPTGVEVCAAMQHGGPFPSTSDSRFTS 481 Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRR 517 VGT AI RF+RPV +QD D+LLP L+ NPL + R Sbjct: 482 VGTGAIYRFVRPVAWQDWDDSLLPPELQSNNPLNIWR 518 Lambda K H 0.319 0.134 0.391 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: 646 Number of extensions: 20 Number of successful extensions: 2 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: 525 Length of database: 527 Length adjustment: 35 Effective length of query: 490 Effective length of database: 492 Effective search space: 241080 Effective search space used: 241080 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 24 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