Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Marino:GFF3684 Length = 489 Score = 302 bits (774), Expect = 1e-86 Identities = 173/480 (36%), Positives = 269/480 (56%), Gaps = 17/480 (3%) Query: 12 QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKE 71 Q F+ G ++ G+T V NPATG+++ V + + AIE+A W A+TA E Sbjct: 9 QNFVHGRFLANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIE 68 Query: 72 RATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGDV 130 R+ L R ++ E D+LA + GKP EA+ ++V A +E+FA A I Sbjct: 69 RSRILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSI---- 124 Query: 131 IPGHQPDKR---LIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPF 187 G+Q D ++P+G+ A I WN+P + K+ PALA G M+ KP+ +TP Sbjct: 125 -EGNQQDLGGDFYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPM 183 Query: 188 SAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK 247 A LAE+ AG+PAGVF+VV G+A ++G LT +P + K+SFTG G+++M+ + Sbjct: 184 GAVKLAEIFTEAGVPAGVFNVVQGAA-EVGQWLTHHPEIAKVSFTGEVATGKKVMAAASS 242 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307 +K V++ELGG +P I+FDDADL+ A+ A++ + G+ C R+++ + +Y F E Sbjct: 243 TLKDVTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIE 302 Query: 308 KLKVAVAK-LKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPME---- 362 +L +K G+ + T G LI K V ++IA LS+GAT+ GG+ E Sbjct: 303 RLLERTRNNIKPGDPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDS 362 Query: 363 --GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420 G F EPTI T+ ++ + KEE FGP+ + F+DE +VIA +N+T+ GLA+ + D Sbjct: 363 KGGYFVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTND 422 Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480 + R RV ++ G+ +N+ S P GG K SG+GRE + I Y +IK + +G+ Sbjct: 423 IRRAHRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYVGM 482 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: 595 Number of extensions: 41 Number of successful extensions: 5 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: 489 Length adjustment: 34 Effective length of query: 446 Effective length of database: 455 Effective search space: 202930 Effective search space used: 202930 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