Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Keio:14450 Length = 490 Score = 311 bits (796), Expect = 4e-89 Identities = 169/477 (35%), Positives = 272/477 (57%), Gaps = 9/477 (1%) Query: 6 TQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWR 65 +++ QQ +I G + A +G+T + NPA G +L TV G + RA+++A + W Sbjct: 2 SRMAEQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIWA 61 Query: 66 ALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAK 124 ++TA ER+ LRR +++ E D+LA+L TL+ GK +E +IV A +E++A Sbjct: 62 SMTAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIP 121 Query: 125 RIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQ 184 + G IP + + ++P+GV A I WN+P + K+ PALAAG M+ KP+ Sbjct: 122 ALEGSQIPLRETSF-VYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEV 180 Query: 185 TPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM-S 243 TP +A LAE+ AG+P GVF+V+ G + G LT +P + K+SFTG G+++M + Sbjct: 181 TPLTALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMAN 240 Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYD 303 A +K+V++ELGG +P IVFDDADLD A + A+++ + ++GQ C R+++ Sbjct: 241 SAASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKA 300 Query: 304 AFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPMEG 363 AF +K+ V +++ G+ + T GPL+ V +IA +GA VL GG ++G Sbjct: 301 AFEQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGDVLKG 360 Query: 364 NFFE------PTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFY 417 + F+ PT+ T+ ++ + +EE FGP+ + ++ E +VI +NDT++GLA+ Sbjct: 361 DGFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIV 420 Query: 418 ARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 DL R RV LE G+ +NT S P GG K SG+GRE ++ Y ++K Sbjct: 421 TADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSYTQVK 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: 553 Number of extensions: 26 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