Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate SMa0247 SMa0247 hypothetical protein
Query= reanno::HerbieS:HSERO_RS19360 (391 letters) >FitnessBrowser__Smeli:SMa0247 Length = 398 Score = 439 bits (1129), Expect = e-128 Identities = 229/387 (59%), Positives = 281/387 (72%), Gaps = 9/387 (2%) Query: 6 SLQAHLPEDHAQATLIGRIWQPGVG-PVLVRIDADGAYDLTLIAATSSELLELDNPAAAV 64 S ++ P D + A L+GR+W G P V I +DLT +AAT S LLE+D A+ Sbjct: 14 SAESIQPADASSAMLVGRVWSKTAGGPCPVLISEGEVFDLTPLAATISALLEIDGLVDAL 73 Query: 65 RSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEEQA 124 R + + +L L AG LLAP DLQAVKA+GVTF SMLERVIEEQA Sbjct: 74 RDPSRFASLGSLDAFLRGE--AGD------LLAPADLQAVKAAGVTFADSMLERVIEEQA 125 Query: 125 RGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAEIF 184 +GD +A+ +R + V+GDNL +V GS +AA +K++L + G+WSQYLEVGIGPDAEIF Sbjct: 126 KGDPLRAQEIRGRLAPVLGDNLKGLVAGSDKAAEVKKLLQELGLWSQYLEVGIGPDAEIF 185 Query: 185 TKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRSAL 244 TKAQPMSSVG G +GIHPKS WNNPEPE+VLA+ S+GK+VGATLGNDVNLRDFEGRSAL Sbjct: 186 TKAQPMSSVGCGAYIGIHPKSDWNNPEPEVVLAVTSKGKIVGATLGNDVNLRDFEGRSAL 245 Query: 245 LLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMISRDP 304 LL KAKDNNASC++GPFIRLFD F+I+DV++AE+++ VDG EGF + G S MS ISR P Sbjct: 246 LLSKAKDNNASCSIGPFIRLFDGAFTIEDVKQAEVSLVVDGKEGFKMTGISPMSAISRSP 305 Query: 305 LQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGALVNT 364 LV + NHQYPDG+V FLGTMFAP +DR G G GFTH++ D V ISTP+LG LVN Sbjct: 306 EDLVSQLLNDNHQYPDGVVFFLGTMFAPVKDRRGTGLGFTHEIGDRVEISTPRLGRLVNW 365 Query: 365 VNFSDQTAPWTFGLTALFKNLADRKLI 391 V+ SD+ W+FGL AL KNLA+R L+ Sbjct: 366 VDHSDRCPKWSFGLGALMKNLAERGLL 392 Lambda K H 0.317 0.134 0.387 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: 480 Number of extensions: 22 Number of successful extensions: 3 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: 391 Length of database: 398 Length adjustment: 31 Effective length of query: 360 Effective length of database: 367 Effective search space: 132120 Effective search space used: 132120 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: 50 (23.9 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