Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate AO353_07805 AO353_07805 betaine-aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07805 Length = 490 Score = 327 bits (837), Expect = 7e-94 Identities = 176/472 (37%), Positives = 276/472 (58%), Gaps = 9/472 (1%) Query: 11 QQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAK 70 Q+ +IDG + DA T + NPA GE+L TV + A+ RA+ +A+K W A+TA Sbjct: 7 QKLYIDGGYSDASGDATFEAINPANGEVLATVQRATFADVERAVVSAEKGQKIWAAMTAM 66 Query: 71 ERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGD 129 ER+ LRR E++ E D+LA L TL+ GK +E + +IV A +E++A I G+ Sbjct: 67 ERSRILRRAVEILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGE 126 Query: 130 VIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSA 189 IP + + ++P+G+ A I WN+P + K+ PALAAG M+ KP+ T + Sbjct: 127 QIP-LRTTSFVYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTT 185 Query: 190 FALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM-SECAKD 248 LAE+ AG+PAGVF+V++GS ++G+ LT +P + K+SFTG T+ G+++M S Sbjct: 186 LKLAEIYTEAGLPAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSS 245 Query: 249 IKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEK 308 +K V++ELGG +P I+FDDADLD+A + A+++ + ++GQ C R+++ + AF K Sbjct: 246 LKDVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAK 305 Query: 309 LKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM------E 362 + VA++++GN + T GPL+ + V +IA +GA +L GG+ + + Sbjct: 306 IVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGERLTEGEFAK 365 Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422 G F PT+ T+ + + +EE FGP+ + ++ E +VI +NDTEFGLA+ RDL Sbjct: 366 GAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTRDLN 425 Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 R RV LE G+ +N S+ P GG K SG+GRE + ++ IK Sbjct: 426 RAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIK 477 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: 573 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: 490 Length adjustment: 34 Effective length of query: 446 Effective length of database: 456 Effective search space: 203376 Effective search space used: 203376 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 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