Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Smeli:SMa2213 Length = 494 Score = 357 bits (917), Expect = e-103 Identities = 194/462 (41%), Positives = 278/462 (60%), Gaps = 9/462 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANE 72 +IDG++V G+ + ++P T V G A + D AV+AA +A + GPW KM E Sbjct: 10 YIDGQWVAPASGEYIETVDPFTARPWALVPRGNAEDADRAVRAAHRAFSQGPWGKMHPTE 69 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKP-TWLSGSID-IPRAAYNFHFFSDYIRTITN 130 R ++++ LI E + L+ +E D G+ ++ I IPR +H+++ + I Sbjct: 70 RGRIIQRFAALIEEHADALADIEVRDNGRLLAEMTHQIRYIPRW---YHYYAGFADKIEG 126 Query: 131 EATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTA 190 D AL+++ P+GV I PWN PLLL + K APALAAGNT+VMKPAE T TA Sbjct: 127 TLHPCDKPALSFSRHEPLGVCVGIVPWNAPLLLFSLKAAPALAAGNTLVMKPAEFTSATA 186 Query: 191 TVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT 250 L E+ AG P GV+N+V G+GP G L HP + FTG T TG + + AAK Sbjct: 187 LKLMELVEKAGFPTGVINVVTGYGPE-VGEPLVTHPLTRHVGFTGSTKTGAHLYSLAAKD 245 Query: 251 LKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEK 310 +KR+S ELGGK+PN++F D++LD + + F G+ C+ GSR+ V R ++ FLEK Sbjct: 246 VKRVSLELGGKSPNIVFGDADLDNAVRGVVGGIFGAVGQTCIAGSRLLVHRSIHDEFLEK 305 Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--EGLEK 368 TK +GDP +T++G + + +E+V GYI +A EG ++ GG RP E Sbjct: 306 LAVFTKTARIGDPRKVETQIGPIANSMQFEKVLGYIDIARREGAELILGGGRPDLEECGT 365 Query: 369 GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLR 428 GYF+EPTI G++ D R+ +EE+FGPV++ I FD EE L ND+ +GL A VWT+D+R Sbjct: 366 GYFIEPTIFAGVSNDMRIAREEVFGPVLSAIVFDEPEEALAIANDSEFGLGAGVWTSDMR 425 Query: 429 RAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGL 470 A +++ ++EAG VWVNT+ TPFGG K+SGIGRE G+ Sbjct: 426 LALKMSERLEAGSVWVNTYRDISYTTPFGGYKKSGIGRENGV 467 Lambda K H 0.318 0.136 0.404 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: 624 Number of extensions: 24 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: 486 Length of database: 494 Length adjustment: 34 Effective length of query: 452 Effective length of database: 460 Effective search space: 207920 Effective search space used: 207920 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