Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Caulo:CCNA_00865 Length = 478 Score = 233 bits (595), Expect = 9e-66 Identities = 149/455 (32%), Positives = 230/455 (50%), Gaps = 10/455 (2%) Query: 71 PAN-NEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDALREKIQLLG 129 P+N N+ +A+V + + + A+KA+ WAD R +++ K+G + + +G Sbjct: 25 PSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDLLDKVGSTIIARSADIG 84 Query: 130 RLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALMEQWNPLGLVG 189 RL++ E GK L EGIGE + Y AG + G L S RPG + +G+ G Sbjct: 85 RLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLESTRPGVEIQTYRQAVGVYG 144 Query: 190 IITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLEDNLLPGAICS 249 +IT +NFP+A+ W A AL GN + K A T A ++A ++ + P + + Sbjct: 145 LITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTP----ATANVLADIMAECGAPAGVFN 200 Query: 250 LTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELGGNNAIIAFEDA 309 + G MG A+ + + V+ +SFTGS VG QVA R + LE+GG N +I +DA Sbjct: 201 MLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQARVQLEMGGKNPLIVLDDA 260 Query: 310 DLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIRVGNPWDPNILY 369 DL + AL + GQRCT RL + + IHD+ V L + +RVG+ DPN Sbjct: 261 DLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAEKVAALRVGDALDPNTQI 320 Query: 370 GPLHTKQAVSMFVQAVEEAKKEGGTVVYGGK--VMDHPGNYVEPTIVTGLVHDAPIVHKE 427 GP ++ + + ++ A EGG VV GG +D+PG YV PT++ I ++E Sbjct: 321 GPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWYVRPTLIADTQAGMRINNEE 380 Query: 428 TFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPT 487 F P+ + K+ EE E N V+ GLS+ I T L + + + G+ VN+ T Sbjct: 381 VFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARHF--QRYARAGMTMVNLAT 438 Query: 488 SGAEIGGAFGGEKHTG-GGRESGSDAWKQYMRRST 521 +G + FGG K + G RE G A + + + T Sbjct: 439 AGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTKT 473 Lambda K H 0.319 0.137 0.417 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: 663 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 539 Length of database: 478 Length adjustment: 34 Effective length of query: 505 Effective length of database: 444 Effective search space: 224220 Effective search space used: 224220 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 (21.7 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