Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate AZOBR_RS31000 AZOBR_RS31000 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__azobra:AZOBR_RS31000 Length = 479 Score = 279 bits (713), Expect = 2e-79 Identities = 173/472 (36%), Positives = 254/472 (53%), Gaps = 14/472 (2%) Query: 11 QQAFIDGAWVDADNGQTI-KVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTA 69 Q +I GAW + G T+ +V NPAT ++ GTV G + +RA+ AA A + Sbjct: 5 QSFYIGGAWTEPAAGATVMEVLNPATEQVSGTVALGGPEDAQRAVAAAHAAFDGFSRTPL 64 Query: 70 KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWF--AEEAKRIY 127 ER L L + D++A +T E G PLA A + A + F A EA R Y Sbjct: 65 NERLELLAAVCALFEKRMDEVADAITEEMGAPLA-ALSKPAQAFMGLAHFKTALEAAREY 123 Query: 128 GDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPF 187 P + ++++P+GV A ITPWN+P I K PALA GCTMVLKP+ P+ Sbjct: 124 ----PFERTRGTTRILREPVGVCAMITPWNWPINQIACKVAPALATGCTMVLKPSEFAPY 179 Query: 188 SAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK 247 SA+ AE+ AG+PAGVF++ G +G L S+P+V +S TGST G + A Sbjct: 180 SAWIFAEILHEAGVPAGVFNMFYGDGAVVGPVLASHPLVDMVSLTGSTRAGASVSHNAAD 239 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307 IK+VSLELGG + I+ + ADL KAV + S N GQ+C +R+Y+ D Sbjct: 240 SIKRVSLELGGKSANIICESADLTKAVTHGVRSMMSNTGQSCNAPSRMYVPASRLDEAET 299 Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAG--GKP--MEG 363 A+L +G+ T GP+ +++ +VQ I + +GAT+L G G+P +E Sbjct: 300 IAAQVCARLVVGDPRGDRTGVGPIANQRQYERVQRLIQAGIEEGATLLCGGPGRPDGLER 359 Query: 364 NFF-EPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422 F+ +PT+ + + + +EE FGP+ + ++D + I +ND+ +GL+ Y YA + Sbjct: 360 GFYAKPTVFSRATDGMTIMREEIFGPVLTIRPYEDIEEAIRSANDSLYGLSGYVYAGTVD 419 Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 VA+ L GMV +N G + APFGG K SG+GRE + G E++LE K Sbjct: 420 EARAVAKRLRTGMVHLN-GASIDLAAPFGGYKQSGIGREWGEVGFEEFLETK 470 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: 602 Number of extensions: 23 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: 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