Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_090272720.1 BLU11_RS07260 aldehyde dehydrogenase family protein
Query= reanno::WCS417:GFF827 (481 letters) >NCBI__GCF_900105005.1:WP_090272720.1 Length = 483 Score = 569 bits (1467), Expect = e-167 Identities = 284/473 (60%), Positives = 353/473 (74%), Gaps = 3/473 (0%) Query: 9 NYINGQWVAGADYC---VNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQ 65 +++NG +V C N NPS +++ +A+AD AI AAR A +W + Q Sbjct: 8 SFVNGVFVEADSQCDVLENRNPSNAEEIVDRFARADAALTEKAIAAARDAAGSWGRTNPQ 67 Query: 66 ARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDY 125 R D LD++GSEIL RR+EL LL+REEGK + EA+GEV RAG FKF+A E LR +G+ Sbjct: 68 VRADILDRIGSEILERRQELAELLSREEGKVVREALGEVERAGRSFKFYAQEVLRANGEK 127 Query: 126 VPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAW 185 SVR GV+V+V + +GVVG+I+PWNFPIAIPAWK APALA+GN VV+KPAELVP AW Sbjct: 128 YESVREGVSVDVFTQPIGVVGIISPWNFPIAIPAWKAAPALAFGNTVVMKPAELVPSSAW 187 Query: 186 ALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQA 245 ALAEIISR+G PAGVFNLV+G GR VGD ++ SPKVD I+FTGS G GRQ+A R Sbjct: 188 ALAEIISRSGMPAGVFNLVIGPGRTVGDTIIRSPKVDAITFTGSEGTGRQVAEIAAQRLI 247 Query: 246 KVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMA 305 +VQLEMGGKNP ++LDDADL A+E+++ +FYSTGQRCTASSRLIVT GIHD+FVA +A Sbjct: 248 RVQLEMGGKNPLVVLDDADLDVAIEVALNGSFYSTGQRCTASSRLIVTTGIHDEFVARLA 307 Query: 306 ERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYL 365 ER ++++VG L + TDIGPVV +QL Q+L YI+ G EGA L+ GG + D Y+ Sbjct: 308 ERTRALRVGDPLCADTDIGPVVDPSQLKQNLAYIESGLQEGATLICGGEYLENDKGAYHF 367 Query: 366 APTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425 +P LF D + MRI REEIFGPV +V++VA+YE AL A DT++ LSAGI TTSLKYA H Sbjct: 368 SPALFVDVQPHMRIYREEIFGPVLSVLKVANYEEALQAAEDTQYSLSAGIVTTSLKYAEH 427 Query: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSY 478 FK+HS AGMVMVNLPTAGVDYH PFGG +GSS G REQG YA++F+T VKT+Y Sbjct: 428 FKKHSSAGMVMVNLPTAGVDYHAPFGGNRGSSLGPREQGTYARQFFTRVKTAY 480 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: 631 Number of extensions: 13 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: 483 Length adjustment: 34 Effective length of query: 447 Effective length of database: 449 Effective search space: 200703 Effective search space used: 200703 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: 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