Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= reanno::acidovorax_3H11:Ac3H11_612 (483 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 275 bits (702), Expect = 3e-78 Identities = 181/478 (37%), Positives = 259/478 (54%), Gaps = 10/478 (2%) Query: 8 LSPRHLINGRW-EIGTTTGISTNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQST 66 LS +HLI G+ G + T E++ A + ++AV +A A W++ + Sbjct: 16 LSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQS 75 Query: 67 PQRRADVLDMIGSELLARKDELGALLAREEGKTL-PEGVAEVARSGQIFKFFAGEALRIQ 125 + R ++ G L A +ELG L+A E GK L E E +F FF G ++ Sbjct: 76 ARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELK 135 Query: 126 GELLASVRQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPA 185 GE + + V V REPVGVVG I PWN P + A K A AL GN+VV K AE P Sbjct: 136 GETIPFNPDMLTVTV-REPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPL 194 Query: 186 CGWALAEIISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQ 245 +AEI++ + LP G FN++ G G E G LV+HP V ++FTGSV TG + +AA++ Sbjct: 195 TVLRVAEIMN-TVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAE 253 Query: 246 RRAKVQLEMGGKNPLIVLADADLDQAVDCALQGSYFS-TGQRCTASSRLIVEAEVHDAFV 304 + V LE+GGK+P+IV ADAD+DQAV AL G F+ GQ CTASSRL V +HD FV Sbjct: 254 KLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFV 313 Query: 305 ARLRNRLASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIA-KSEGA-EHVWGGERLE-R 361 A+++ ++ ++ +G L+ T++G +V D QL + YI I +++GA +HV + + Sbjct: 314 AKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPK 373 Query: 362 PTPGHYMSPALFLA-RPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTT 420 G ++ P +F + R+ +EEIFGPV V++ DY+ LA AND+ +GL A I T Sbjct: 374 LAKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTR 433 Query: 421 SLKRAMHFKRHAAVGMTMVNLPTAGVDFHVPFGGRKESSYGAREQGRYAAEFYTTVKT 478 K AM + G VN V + +GG K S G E +T KT Sbjct: 434 DFKLAMDATKRLEAGFVQVN-QNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKT 490 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: 517 Number of extensions: 29 Number of successful extensions: 5 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: 496 Length adjustment: 34 Effective length of query: 449 Effective length of database: 462 Effective search space: 207438 Effective search space used: 207438 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