Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 277 bits (708), Expect = 7e-79 Identities = 174/481 (36%), Positives = 252/481 (52%), Gaps = 7/481 (1%) Query: 18 IEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSR 77 + G+ I G+ A GE FE +P G ++G A D AV +A+A W++ Sbjct: 16 LSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKD--WAK 73 Query: 78 LAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDK 137 + R + +L H EEL L L+ GK + ++ A ++ G + Sbjct: 74 QSARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSE 133 Query: 138 IYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSP 197 + E D L + REPVGVVG I+PWN PL++ K AL GNSV++K +E++P Sbjct: 134 LKGETIPFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAP 193 Query: 198 LTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSG 257 LT +R+AE+ + +P G+ N+L G+G G L H DV + FTGS + + ++ + Sbjct: 194 LTVLRVAEI-MNTVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGR-IVYKAA 251 Query: 258 ESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDK 317 + V LE GGKSP IV ADA Q A A AG QG+ CTA SRL V SI D+ Sbjct: 252 AEKLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDE 311 Query: 318 FLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGH--ADGARLVAGGKRTL 375 F+ V + A G+PLD T++G +V Q+ V SYI+ G + V T Sbjct: 312 FVAKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTD 371 Query: 376 QETG-GTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVW 434 + G +V+P IF G+ N+ ++ QEEIFGPV +VI++ E+ +A AND+ YGLAA++W Sbjct: 372 PKLAKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIW 431 Query: 435 TADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATW 494 T D A + L AG V VNQ +GG K SG G++ SL + ++ K T Sbjct: 432 TRDFKLAMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKTI 491 Query: 495 I 495 I Sbjct: 492 I 492 Lambda K H 0.316 0.132 0.390 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: 584 Number of extensions: 29 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: 497 Length of database: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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