Align Rhizopine-binding protein (characterized, see rationale)
to candidate SM_b20712 SM_b20712 rhizopine uptake ABC transporter substrate-binding protein precursor
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__Smeli:SM_b20712 Length = 309 Score = 279 bits (713), Expect = 7e-80 Identities = 149/297 (50%), Positives = 212/297 (71%), Gaps = 5/297 (1%) Query: 15 MLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVKQLSQ 74 +L S AA A+ IGVSM+ FDD +LT LR M + AK++ DGV+LQ EDA++DV KQ SQ Sbjct: 12 VLMSTAAHAET-IGVSMALFDDNFLTVLRSGMQEYAKTL-DGVELQVEDAQNDVAKQQSQ 69 Query: 75 VESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK-LPKGVITVASND 133 +++FI+ VDAI+VNPVDT AT +++ A AGIPLVYVNR P ++ LP VASN+ Sbjct: 70 IQNFIAAGVDAIIVNPVDTDATAAMSKIAADAGIPLVYVNREPVNVDTLPDKQAFVASNE 129 Query: 134 LEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVLA--KYPGIKIDQEQTG 191 E+G +Q + + + + GKG V+++G+L+N + RTK + +V+A + GI+I +EQT Sbjct: 130 QESGTLQTKEICKMLGGKGKAVVMMGELSNQAARMRTKDIHDVIATDECKGIEIVEEQTA 189 Query: 192 TWSRDKGMTLVNDWLTQGRKFDAIVSNNDEMAIGAAMALKQAGVEKGSVLIAGVDGTPDG 251 WSR +G L+ +WL+ G +FDA++SNNDEMAIGA ALK AG SV+I G+D T D Sbjct: 190 NWSRTQGSDLMTNWLSAGLEFDAVISNNDEMAIGAIQALKAAGRSMDSVVIGGIDATQDA 249 Query: 252 LRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENVDQFK 308 L A+ GDL V+VFQ+A GQ S+DAA+K+AK EPVE+ V++P+ L+T +N+ Q++ Sbjct: 250 LAAMAAGDLDVTVFQNAAGQGKGSVDAALKLAKGEPVEKKVYIPFELVTKDNLAQYQ 306 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: 267 Number of extensions: 16 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: 308 Length of database: 309 Length adjustment: 27 Effective length of query: 281 Effective length of database: 282 Effective search space: 79242 Effective search space used: 79242 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