Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_006897513.1 BJL86_RS01995 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_001659785.1:WP_006897513.1 Length = 493 Score = 241 bits (614), Expect = 6e-68 Identities = 158/490 (32%), Positives = 245/490 (50%), Gaps = 25/490 (5%) Query: 37 YPLIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQT--WRNVNP 94 Y L I+G+ V T++ +P ++ +++K + A+++A AF + WR Sbjct: 4 YSLFIDGKSVDTDETYDVVSPG-DGTVIATLAKGGTAEVDAAVEAAAAAFASSGWRETPM 62 Query: 95 EERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRG 154 ERA ++ +AA I R E S E G P + A ++ F + R +L R Sbjct: 63 HERAAVIDRAADAIEARAEEISLLASRENGTPVRLAQG---LSVGFPVMHIRYFADLAR- 118 Query: 155 KEILSRPGEQNRYFY-----TPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPAST 209 + + +P + P+GV I PWNF L + V ++ I GN+VVLK Sbjct: 119 RHVTDQPTMVSGSVVGIIRREPIGVVAGIVPWNFPLLLTVWKSIPAIAAGNSVVLKADEK 178 Query: 210 TPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYER 269 TP A EVL+ AGLP GV N + G GAEVG +L HPK ++FTGS G + Sbjct: 179 TPSTALILAEVLKAAGLPDGVFNVITGDGAEVGGHLTKHPKVRKVSFTGSTATGRTVMAN 238 Query: 270 AAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIH 329 AA +K+V +E+GGK +V DADLDLA + L + +GQ C +G+R +H Sbjct: 239 AA------ERVKKVTMELGGKGANIVLPDADLDLAVDGSLWAFLVHAGQACESGTRLFVH 292 Query: 330 KDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTG-- 387 + +Y E +++ V A LT+GDPT+ +GP+++ E++ +I+ GKK+G + Sbjct: 293 RTIYREFVDRLVQRASQLTIGDPTDMSTDIGPLMNRAQRERVEGFIDSGKKDGATVAFQA 352 Query: 388 --GEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLT 445 + G ++ PTI D+ P+ I EEIFGPVV+ +D D + AN +EYGL+ Sbjct: 353 ELPADLNREGMWVPPTIFTDVTPDMKITTEEIFGPVVSVMAYDDIDAVVAEANTSEYGLS 412 Query: 446 GAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALH 505 V T + G ++ N A+ G PFGG K SG + GP+ + + Sbjct: 413 AGVWTTDYTVAMDLAHRLEAGTVWIND--WHALSGQLPFGGVKQSGF-GREMGPNAINEY 469 Query: 506 MQAKTVSEMY 515 K+++ Y Sbjct: 470 TNEKSIAIDY 479 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: 605 Number of extensions: 22 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: 493 Length adjustment: 34 Effective length of query: 481 Effective length of database: 459 Effective search space: 220779 Effective search space used: 220779 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