Align Rhizopine-binding protein (characterized, see rationale)
to candidate HSERO_RS05170 HSERO_RS05170 LacI family transcription regulator
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__HerbieS:HSERO_RS05170 Length = 324 Score = 118 bits (295), Expect = 2e-31 Identities = 90/299 (30%), Positives = 148/299 (49%), Gaps = 17/299 (5%) Query: 13 SLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVKQL 72 ++ L + AA L +G S + W T S+ AK GV L+F DA+ Q+ Sbjct: 21 AMSLPAFAADKPLTMGFSQVGAESEWRTANTVSIKDAAKQA--GVNLKFADAQQKQENQV 78 Query: 73 SQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLKLPKGVITVASN 132 + SFI+QKVD I +PV + + A A IP++ +R + V + S+ Sbjct: 79 KAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKSLYVTFIGSD 138 Query: 133 DLEAGQMQMQYLAEKMK----GKGDIVILLGDLANNSTTNRTKGVKEVLAKYPGIKIDQE 188 +E G+ ++L EK K G +IV L G + + +R G +EV+ P +KI + Sbjct: 139 FVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKGEPRLKIIRS 198 Query: 189 QTGTWSRDKGMTLVNDWL-TQGRKFDAIVSNNDEMAIGAAMALKQAGVEKG-SVLIAGVD 246 QTG ++R KG ++ +L +G+K + + ++ND+MAIGA A+++AG++ G ++I +D Sbjct: 199 QTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGMKPGKDIIIISID 258 Query: 247 GTPDGLRAVKKGDLAVSV-FQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENV 304 G A+ G L V+V G + I +K K VP R+ T E + Sbjct: 259 GVKGAFEAMMAGKLNVTVECSPLLGPQLMQIAKDIKAGKE--------VPKRITTEEGI 309 Lambda K H 0.315 0.130 0.360 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: 219 Number of extensions: 13 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: 308 Length of database: 324 Length adjustment: 27 Effective length of query: 281 Effective length of database: 297 Effective search space: 83457 Effective search space used: 83457 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 (21.5 bits) S2: 48 (23.1 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