Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Caulo:CCNA_00865 Length = 478 Score = 255 bits (652), Expect = 2e-72 Identities = 157/474 (33%), Positives = 243/474 (51%), Gaps = 13/474 (2%) Query: 41 INGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANI 100 I GERV + +S NP+ + +V V Q + A+ +A +AF W + +PE R+++ Sbjct: 9 IGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDL 68 Query: 101 LVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSR 160 L K + I R + L E GK E +T A +Y+A + + + +R Sbjct: 69 LDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLESTR 128 Query: 161 PGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEV 220 PG + + + +GV I+PWNF +AI A + GNTVV+KPA TP A ++ Sbjct: 129 PGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLADI 188 Query: 221 LEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHL 280 + + G P GV N + G G+ +GD L+ H ++FTGS+ VG ++ AAV R Sbjct: 189 MAECGAPAGVFNMLFGRGS-MGDALIKHKDVDGVSFTGSQGVGAQV-AAAAVARQA---- 242 Query: 281 KRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKT 340 RV +EMGGK+ ++V DADL+ A L +F +GQ+C+A SR ++ ++D+ + Sbjct: 243 -RVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALL 301 Query: 341 VALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKE-GRLMTGGEGD--SSTGFF 397 L VGD + + +GP + E E YI+I E GR++TGG+ + G++ Sbjct: 302 AEKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWY 361 Query: 398 IQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIE 457 ++PT+IAD I EE+FGPV + + ++ ALEIAN E+GL+ + T + H Sbjct: 362 VRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHAR 421 Query: 458 QAKREFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510 +R G N G V YH PFGG K S ++ G + Q KT Sbjct: 422 HFQRYARAGMTMVNLATAG--VDYHVPFGGTKSSSYGAREQGFAAVEFFTQTKT 473 Lambda K H 0.316 0.134 0.388 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: 590 Number of extensions: 28 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: 515 Length of database: 478 Length adjustment: 34 Effective length of query: 481 Effective length of database: 444 Effective search space: 213564 Effective search space used: 213564 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 (21.6 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