Align Ribose import permease protein RbsC (characterized)
to candidate WP_068006265.1 PsAD2_RS12365 ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >NCBI__GCF_001623255.1:WP_068006265.1 Length = 368 Score = 148 bits (373), Expect = 2e-40 Identities = 103/338 (30%), Positives = 165/338 (48%), Gaps = 37/338 (10%) Query: 17 LMEQKSLIAL----LVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGI 72 LM++ L AL LV I T P F++ N + S I+A+G L+++ Sbjct: 22 LMKRPELGALAGLALVTIFFAFTADPKMFSLAGFLNFMTPASQLGILAIGAALLMIGGEF 81 Query: 73 DLSVGSLLALTGAV-AASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATL 131 DLSVGS++A TG + A++V E+ A+ + AA+GAV G IV + + +FI TL Sbjct: 82 DLSVGSMVAFTGLIFGAAMVTFELPLYAAIIVTFMVAAAMGAVNGQIVIRTGLPSFIVTL 141 Query: 132 VMMLLLRGVTMV----YTNGSPVNTGFTENAD---------------LFGW--------- 163 + +LRG+++V T GS G E + LF W Sbjct: 142 AFLFILRGLSLVGLKAATGGSTQLRGVREKVEGSWIADFFSGEAFTPLFYWLAENGLVDT 201 Query: 164 FGIGRPL--GVPTPV-WIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIK 220 F G+P G+P + W + +A W +L +R G +I+A GG+ +A SG+ V ++K Sbjct: 202 FKSGKPKVDGIPVEIIWFTLLAGVATWILLR-SRFGSWIFASGGDSSAASNSGVPVRRVK 260 Query: 221 IIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLI 280 + ++ A+L I+ V S G E +AI A V+GG+ L GG G +G Sbjct: 261 MYLFMFTACCAALVAILTVMDAGSTDARRGFQKEFEAIIAAVIGGSLLTGGYGSAIGAFF 320 Query: 281 GALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDN 318 G++I G + GL+ + + ++ ++LLAVL +N Sbjct: 321 GSIIFGMVLIGLSYTNIDQDWYLVFLGSMLLLAVLFNN 358 Lambda K H 0.324 0.139 0.393 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: 250 Number of extensions: 17 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: 321 Length of database: 368 Length adjustment: 29 Effective length of query: 292 Effective length of database: 339 Effective search space: 98988 Effective search space used: 98988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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