Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >FitnessBrowser__Pedo557:CA265_RS19780 Length = 513 Score = 190 bits (482), Expect = 1e-52 Identities = 143/466 (30%), Positives = 227/466 (48%), Gaps = 25/466 (5%) Query: 36 TFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLK 95 T E SPVDG+L+ A D V A+ F + W + KR + +F L+ Sbjct: 35 TLESFSPVDGKLIASAKIATADDYDAVVLKAQEAFTA--WRSVPAPKRGEIVRQFGDALR 92 Query: 96 QHAEELALLETLDMGKPISDSL-----YIDVPGAAQALSWSGEAIDKIYDEVAATPHDQL 150 ++ + L L + +MGK + + ID+ A LS + + + ++Q Sbjct: 93 ENKDALGTLVSYEMGKSLQEGFGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQW 152 Query: 151 GLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIR----IAEL 206 P+G+VG I +NFP+ + W AL GN I KPSEK+PLTAI IA++ Sbjct: 153 -----HPLGIVGIISAFNFPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQHIIAKV 207 Query: 207 AVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESNMKRVWL 266 + I +GV N++ G VG+ + + + TGST++ K + G + + + L Sbjct: 208 FKDNDIAEGVCNLILG-DREVGERMTNDGRIPLISATGSTRMGKAVGAAVG-ARLGKSLL 265 Query: 267 EAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEAL 326 E GG + I+ A A GA+ G+ CT+ RL++ S+ D F +++A Sbjct: 266 ELGGNNAIIISEHADLDMSLIGAVFGAVG-TAGQRCTSTRRLIIHESVYDAFTAKLVKAY 324 Query: 327 KAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGKRTLQE--TGGTYVE 384 + G+PLD +VG L+DT + L I A+G V G + T G YV+ Sbjct: 325 GQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSGCYVK 384 Query: 385 PTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADISKAH-- 442 P I + V N KI Q E F P+L +I++ + +EAIA+ N P GL++A+ T ++ +A Sbjct: 385 PCIAE-VQNDFKIVQHETFAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLREAEQF 443 Query: 443 LTARALRAGSVWVN-QYDGGDMTAPFGGFKQSGNGRDKSLHAFDKY 487 L+A+ G VN G ++ FGG K++G GR+ A+ Y Sbjct: 444 LSAKGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWRAY 489 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: 644 Number of extensions: 35 Number of successful extensions: 5 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: 513 Length adjustment: 34 Effective length of query: 463 Effective length of database: 479 Effective search space: 221777 Effective search space used: 221777 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