Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011842150.1 RSPH17029_RS16005 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_000015985.1:WP_011842150.1 Length = 495 Score = 293 bits (749), Expect = 1e-83 Identities = 172/470 (36%), Positives = 260/470 (55%), Gaps = 10/470 (2%) Query: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPA--WRALTAKE 71 FIDG +VD+ +G+T P G L V AA+ A+ +A +A A W + + Sbjct: 21 FIDGQYVDSLSGETFACIYPGDGRPLTDVASCNAADVDVAVRSARRAFEAGVWSRMAPAD 80 Query: 72 RATKLRRWYELIIENQDDLARLMTLEQGKPLAEA-KGEIVYAASFIEWFAEEAKRIYGDV 130 R L R+ ELI+ N+++LA L TL GKP+A A G++V AA+ I W+AE ++YG+V Sbjct: 81 RRRILLRFSELILANREELALLETLNVGKPIANAYNGDVVSAAACIAWYAEAIDKVYGEV 140 Query: 131 IPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAF 190 D +V+++P+G+ AA+ PWN+P +M K GPALA G +++LKPA Q+PF+A Sbjct: 141 AATAH-DMTTLVMREPLGIVAAVVPWNYPMSMAAWKLGPALATGNSVILKPAEQSPFTAL 199 Query: 191 ALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK-DI 249 ELA AG+P GV +VV G G L + V + FTGSTE+G+ M + +I Sbjct: 200 KFGELAIEAGMPPGVLNVVPGLGHIAGKALGLHMDVDCVGFTGSTEVGKYFMQYSGQSNI 259 Query: 250 KKVSLELGGNAPFIVFDDA-DLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEK 308 K++ LELGG +P +V D DLD A G + N GQ C +RL + + ++D EK Sbjct: 260 KRIGLELGGKSPQVVLADCDDLDAAAAGIAAGIFANTGQVCNAGSRLIVDEKIHDQLLEK 319 Query: 309 LKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGG---KPMEGNF 365 + G+ L+ T G ++ E+ + +V +I + GA + GG K G F Sbjct: 320 IAAQAKVFAPGDPLDTATRMGSMVSEEQMDRVLGYIDAGRADGARPVIGGGRVKTETGGF 379 Query: 366 F-EPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRV 424 + EPTI V N+ +A+EE FGP+ K + +A++NDT +GLA + + Sbjct: 380 YIEPTIFEGVRNDMKIAQEEIFGPVLSAIPVKGFDEAMAVANDTVYGLAGAVWTGSVKNA 439 Query: 425 FRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 R A++L G+V VN + PFGG K SG GR+ S + ++ Y ++K Sbjct: 440 HRAAKSLRAGVVWVNCFDRGSLAVPFGGFKQSGFGRDKSLHAMDKYTDLK 489 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: 563 Number of extensions: 30 Number of successful extensions: 7 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: 495 Length adjustment: 34 Effective length of query: 446 Effective length of database: 461 Effective search space: 205606 Effective search space used: 205606 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. 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