Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate H281DRAFT_02333 H281DRAFT_02333 aldehyde dehydrogenase (NAD+)
Query= reanno::acidovorax_3H11:Ac3H11_612 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_02333 Length = 482 Score = 576 bits (1485), Expect = e-169 Identities = 289/471 (61%), Positives = 353/471 (74%), Gaps = 5/471 (1%) Query: 11 RHLINGRWEIGTTTGISTNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQRR 70 RH ING WE G TTG+S NPSD E V EY RAD QT+ A+ AA+ A W+ S+ QRR Sbjct: 15 RHYINGGWETGATTGVSLNPSDLDEPVGEYVRADVRQTDSAIEAASAAFREWALSSAQRR 74 Query: 71 ADVLDMIGSELLARKDELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELLA 130 AD LD IGSE+LAR+DELG LLARE GKTLPE +AE R+GQ FK A +A R E LA Sbjct: 75 ADALDAIGSEMLARRDELGRLLAREVGKTLPEALAEATRAGQTFKLLAADAQRAYAEPLA 134 Query: 131 SVRQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWAL 190 S R GV++D+TREP+GVVGIIAPW+ P AI A KI ALA+GN VV+KPAE PAC AL Sbjct: 135 SARAGVEIDMTREPLGVVGIIAPWSAPLAIAAGKIGAALAHGNCVVYKPAESTPACAAAL 194 Query: 191 AEIISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAKV 250 A I+SR+GLPAG FNL+MGSGR+VG +V HPLV A+SF+GS TG R+L+AA+ R+A+V Sbjct: 195 ASIVSRAGLPAGVFNLVMGSGRQVGARIVAHPLVAAISFSGSAETGTRVLQAAAARQARV 254 Query: 251 QLEMGGKNPLIVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRNR 310 QLEMGGKNP +VLADADLD AVD AL G+Y STGQR TA++RLIVE + + FV L+ + Sbjct: 255 QLEMGGKNPFVVLADADLDSAVDAALTGAYGSTGQRSTAAARLIVERSIFEPFVDALQTK 314 Query: 311 LASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGHYMSP 370 LA L V HAL+ G +MGPV + QL ++L Y++I K EGA+ + GG +LER T G++ P Sbjct: 315 LARLNVDHALKHGADMGPVANAAQLERDLDYVEIGKQEGAQLLHGGRQLERATRGYFFEP 374 Query: 371 ALFLARPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFKR 430 ALF+ PEHR+AREEIFGP+A VLRADDYDHAL LANDT +GLCAGICT SL RA HF+R Sbjct: 375 ALFVGEPEHRIAREEIFGPLAVVLRADDYDHALHLANDTAYGLCAGICTRSLSRARHFRR 434 Query: 431 HAAVGMTMVNLPTAGVDFHVPFGGRKESSYGAREQGRYAAEFYTTVKTGYM 481 H G+ +NLPT+ V+ H P GGRK S+YG+ + A F+T VKT Y+ Sbjct: 435 HVHSGLVTINLPTSAVEHHAPGGGRKASAYGSTD-----AAFWTAVKTAYV 480 Lambda K H 0.320 0.135 0.400 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: 671 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: 483 Length of database: 482 Length adjustment: 34 Effective length of query: 449 Effective length of database: 448 Effective search space: 201152 Effective search space used: 201152 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