Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__Marino:GFF3684 Length = 489 Score = 338 bits (868), Expect = 2e-97 Identities = 185/481 (38%), Positives = 276/481 (57%), Gaps = 14/481 (2%) Query: 22 NYIDGNFVTSAS--SFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQD 79 N++ G F+ +++ +F +NP G++I +V AD + V +A + + A W ++ + Sbjct: 10 NFVHGRFLANSTGETFPVVNPATGQVIYEVEVAD-ESVQQAAIESARAGFAEWSAMTAIE 68 Query: 80 RAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDL 139 R+ ++ + ++ R +E AAEV DTG+P +A +D+ FA LA + Sbjct: 69 RSRILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPS----- 123 Query: 140 FEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199 E + D G YT R+PLG+ I WN P+ + WK APALACGN ++ KPSEE+P Sbjct: 124 IEGNQQDLGGDFYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPM 183 Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259 A LAE+ +AGVP GVFN++ G + G++LT HP I+ ++FTGE TG +M A + Sbjct: 184 GAVKLAEIFTEAGVPAGVFNVVQGAAE--VGQWLTHHPEIAKVSFTGEVATGKKVMAAAS 241 Query: 260 DGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFV 319 +K+V+ ELGGK+ ++F DADL+ AI + +F G++C RV+VH ++ F+ Sbjct: 242 STLKDVTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFI 301 Query: 320 SGLKVEAERLVV-GYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFND 378 L + G P N G LIS HRD VL Y + EGAT+ GG F Sbjct: 302 ERLLERTRNNIKPGDPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRA--FEP 359 Query: 379 ERDQGAY-VQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIW 437 E +G Y V+PTI+T +D V EEIFGPV + F DEDEVI R N+++ GLA ++ Sbjct: 360 EDSKGGYFVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVF 419 Query: 438 TTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANIC 497 T ++ RAHRV QI G+ W+N++ P GG KLSG+GRE GR ++ Y+ I ++ Sbjct: 420 TNDIRRAHRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVY 479 Query: 498 I 498 + Sbjct: 480 V 480 Lambda K H 0.318 0.135 0.405 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: 579 Number of extensions: 34 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: 500 Length of database: 489 Length adjustment: 34 Effective length of query: 466 Effective length of database: 455 Effective search space: 212030 Effective search space used: 212030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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