Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Caulo:CCNA_00424 Length = 479 Score = 286 bits (731), Expect = 1e-81 Identities = 169/477 (35%), Positives = 251/477 (52%), Gaps = 33/477 (6%) Query: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 +IDGAWVD T+ V NPAT E+ G + A+ +A+ AA KA ++ + +ER Sbjct: 8 YIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAFASFSQTSREERI 67 Query: 74 TKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYG----- 128 L R + +D+A+ +T E G P W A+ A+ G Sbjct: 68 DILERIIAEYQKRFEDMAKAITEEMGAPA---------------WLAQRAQAAMGIGHVQ 112 Query: 129 ---DVIPGHQPDK---RLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 V+ G++ ++ ++K+PIGV A ITPWN+P I K GPA+A GCTMVLKP+ Sbjct: 113 TAAAVLKGYKFEEDRGTTRIVKEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPS 172 Query: 183 SQTPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM 242 PFS + E+ AG+PAGVF++V+G +G+ L+ +P V +SFTGST G ++ Sbjct: 173 EIAPFSGYIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAGIEVA 232 Query: 243 SECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVY 302 A +K+V ELGG +P I+ DDAD +AV G + S N+GQ+C R+ + Sbjct: 233 KNAAPTVKRVHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARM 292 Query: 303 DAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAG--GKP 360 D K A +G+ GP++ E K+Q I + +GAT++ G G+P Sbjct: 293 DEVIAIAKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRP 351 Query: 361 M---EGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFY 417 +G + +PT+ NV N +AKEE FGP+ + + + + + NDTE+GLA+Y Sbjct: 352 EGLDKGYYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVS 411 Query: 418 ARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 D V +VA L G V +N G + +APFGG K SG GRE + ++LE K Sbjct: 412 GGDQDEVRKVASRLRAGQVTLN-GAGPDLMAPFGGYKMSGNGREWGDHAFGEFLETK 467 Lambda K H 0.317 0.135 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: 561 Number of extensions: 20 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: 480 Length of database: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 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 (21.7 bits) S2: 51 (24.3 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