Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_102106082.1 C0029_RS01630 aldehyde dehydrogenase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_002869505.1:WP_102106082.1 Length = 474 Score = 288 bits (738), Expect = 2e-82 Identities = 161/467 (34%), Positives = 255/467 (54%), Gaps = 12/467 (2%) Query: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 +I+G WVD +++ V NPAT ++ + AA+ +A +AA+ A ++ + +ER Sbjct: 8 YINGEWVDPVEPKSMDVINPATEKVCARISIGSAADVDKAAKAANAAFASFSRTSREERV 67 Query: 74 TKLRRWYELIIENQDDLARLMTLEQGKPLA-EAKGEIVYAASFIEWFAEEAKRIYGDVIP 132 L E+ + +D+A +T E G P A + + E K + Sbjct: 68 ELLGAICEVYQKRYNDIADAITEEMGAPTALSVHAQAATGIGHLSTAMEILKTFEFEEAA 127 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192 GH V K+PIGV ITPWN+P IT K GPALA GCT+VLKP+ P + Sbjct: 128 GHSR-----VFKEPIGVCGMITPWNWPINQITCKVGPALAVGCTVVLKPSEVAPLCGYIF 182 Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV 252 AE+ AG+PAGVF++++G +G+ ++S+P++ +SFTGST G + A +K+V Sbjct: 183 AEVMHEAGVPAGVFNMINGDGAGVGTAISSHPLIEMVSFTGSTRAGSLVAQNAAPSVKRV 242 Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVA 312 + ELGG +P I+ DD +L++AV ++ ++N GQ+C +R+ + + A A Sbjct: 243 TQELGGKSPNILLDDVNLEEAVTRGVMHMFQNTGQSCNAPSRMLVPRAKMEEAAAIAANA 302 Query: 313 VAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAG--GKPM---EGNFFE 367 A + +G+ GT+ GP++ E K+Q I + +GA + G G+P +G F + Sbjct: 303 AATVVVGDPRAEGTSMGPVVSEVQWNKIQGLIQAGIDEGAVLACGGVGRPEGIDKGYFVQ 362 Query: 368 PTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRV 427 PT+ +NV N+ +A+EE FGP+ + + + IA++NDT +GLA Y D+ +V V Sbjct: 363 PTVFSNVNNDMTIAREEIFGPVLCIMPYDSLDEAIAIANDTPYGLAGYVQGEDMDQVMSV 422 Query: 428 AEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 A + G + +N G + + PFGG K SG GRE +G DYLEIK Sbjct: 423 AGKIRAGNININ-GQSGDLMTPFGGYKQSGNGREWGAHGFTDYLEIK 468 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: 524 Number of extensions: 19 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: 474 Length adjustment: 33 Effective length of query: 447 Effective length of database: 441 Effective search space: 197127 Effective search space used: 197127 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 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