Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 253 bits (646), Expect = 1e-71 Identities = 157/450 (34%), Positives = 238/450 (52%), Gaps = 20/450 (4%) Query: 47 TTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAA 106 TT I PA +Q + +V A + +KA+ +A A + W ++ ER IL +AA Sbjct: 21 TTGTPIPVIYPATGEQ-IATVYAATPAIVDKALAAAHRAQKAWAAMSGTERGRILRRAAD 79 Query: 107 IIRRRKHEFSAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIELNRGKEILSRPGEQN 165 ++R R H+ S ++ GKP++E A D D LEY+ L G+ I + GE Sbjct: 80 MMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLT-GEHI--QLGED- 135 Query: 166 RYFYT---PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLE 222 + YT P+GV V I WN+ I + GN +V KP+ TTP+ A K E+L Sbjct: 136 -WVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKVAEILH 194 Query: 223 DAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKR 282 +AGLP G+ N V G G EVG LV P+ + ++ TGS G ++Y AA +K Sbjct: 195 EAGLPAGIYNVVQGLG-EVGASLVTDPRVAKVSLTGSVPTGKKVYAAAA------EQMKH 247 Query: 283 VIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVA 342 V +E+GGK +++ DADL+ A ++ F SGQ CS G+R + K + + L++ Sbjct: 248 VTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTE 307 Query: 343 LAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGDSSTGFFIQPT 401 VGDP + GP++ EK + ++ YIE G+ EG RL+ GG + GF++QPT Sbjct: 308 RLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQPT 367 Query: 402 IIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKR 461 + AD+ + +I +EEIFGPV+A + A+ AN+TE+GL+ V TR+ + + Sbjct: 368 VFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIA 427 Query: 462 EFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 + G+ + N + PFGG KMSG Sbjct: 428 QLEAGSCFINSYNDAPVEA--PFGGTKMSG 455 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: 610 Number of extensions: 32 Number of successful extensions: 6 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: 485 Length adjustment: 34 Effective length of query: 481 Effective length of database: 451 Effective search space: 216931 Effective search space used: 216931 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 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