Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 332 bits (851), Expect = 2e-95 Identities = 182/473 (38%), Positives = 281/473 (59%), Gaps = 9/473 (1%) Query: 10 RQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTA 69 RQQ +I G +VDA + +T + NPA GE+L V + GAA+ RA+E+A++ W ALT Sbjct: 6 RQQLYIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTG 65 Query: 70 KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYG 128 ERA +RR +L+ E D+LA L TL+ GKPL+E + +IV A +E++A A I G Sbjct: 66 IERARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEG 125 Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFS 188 + IP + + ++P+GV A I WN+P + KA PALAAG M+ KP+ T S Sbjct: 126 EQIP-LRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLS 184 Query: 189 AFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECA-K 247 A LAE+ AG+P GVF+V++GS +G+ +T +P + K+SFTG G+++M+ A Sbjct: 185 ALKLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASS 244 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307 +K V++ELGG +P I+ +DADLD+A + A+++ + ++GQ C R+++ G+ AF Sbjct: 245 SLKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEA 304 Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM------ 361 KL V ++++G+ + T GPL+ + V ++IA + GA +L GG+ + Sbjct: 305 KLLERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEYA 364 Query: 362 EGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDL 421 +G F PTI ++ ++ A+ EE FGP+ L ++DE +VI +NDTE+GLA+ DL Sbjct: 365 KGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADL 424 Query: 422 GRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 R R+ LE G+ +NT S P GG K SG+GRE + Y +K Sbjct: 425 ARAHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVK 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: 554 Number of extensions: 25 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