Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_004265886.1 C665_RS00960 2-hydroxymuconic semialdehyde dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_612 (483 letters) >NCBI__GCF_000310185.1:WP_004265886.1 Length = 486 Score = 254 bits (649), Expect = 5e-72 Identities = 164/461 (35%), Positives = 239/461 (51%), Gaps = 17/461 (3%) Query: 29 NPSDTREVVAEYARADRNQTELAVRAAADALP-TWSQSTPQRRADVLDMIGSELLARKDE 87 NP + + V+ A A + + AV+AA AL W + Q+R ++L+ + E+ R D+ Sbjct: 25 NPINNK-VIGMVAEAGEKEVDAAVKAAKAALKGPWGSMSLQKRIELLEALVVEINNRFDD 83 Query: 88 LGALLAREEGKTLPEGVA---EVARSGQIFKFFAGEALRIQGEL--LASVRQGVQVDVT- 141 + GK P+ +A ++ R FK FA + E + + G ++ Sbjct: 84 FLEAECADTGK--PKSMASHVDIPRGAANFKVFADMVKNVPTEFFEMTTPDGGKAINYGY 141 Query: 142 REPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAEIISRSGLPA 201 R PVGVVG+I PWN P + WK+ PALA GNTVV KP+E P L E++++ G+P Sbjct: 142 RRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEDTPRTAALLGEVMNKVGIPK 201 Query: 202 GAFNLIMGSG-REVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAKVQLEMGGKNPL 260 G +N++ G G G L HP V+AL+FTG TG+ I++AA+ V LEMGGKN Sbjct: 202 GVYNVVNGFGANSAGAFLTAHPDVDALTFTGETRTGEVIMKAAANGSRPVSLEMGGKNAA 261 Query: 261 IVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRNRLASLKVGHAL 320 IV AD D D+A++ L+ + + GQ C + R+ VE + D FVA L+ +K+G Sbjct: 262 IVFADCDFDKAIEGTLRSVFLNCGQVCLGTERVYVERPIFDKFVAALKAGAEGMKIGVPD 321 Query: 321 ERGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERP---TPGHYMSPALFLARP 377 + GP+V + L Y +A EGA V GG + P G ++ P ++ P Sbjct: 322 DPAANFGPLVSKKHQEKVLSYYKVAVEEGATVVTGGGVPQMPGELADGCWVQPTIWTGLP 381 Query: 378 E-HRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFKRHAAVGM 436 E RV +EEIFGP + D + L AND +GL I T + RA + VG+ Sbjct: 382 ETARVIKEEIFGPCCHIAPFDTEEEVLEKANDNKYGLACAIWTQDVSRAHRVAQKMEVGI 441 Query: 437 TMVNLPTAGVDFHVPFGGRKESSYGAREQGRYAAEFYTTVK 477 + VN D PFGG K+S G RE G ++ EFYT +K Sbjct: 442 SWVNSWFLR-DLRTPFGGSKQSGIG-REGGVHSLEFYTDLK 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: 534 Number of extensions: 25 Number of successful extensions: 4 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: 486 Length adjustment: 34 Effective length of query: 449 Effective length of database: 452 Effective search space: 202948 Effective search space used: 202948 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