Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate RR42_RS22880 RR42_RS22880 ABC transporter permease
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Cup4G11:RR42_RS22880 Length = 301 Score = 152 bits (384), Expect = 9e-42 Identities = 91/277 (32%), Positives = 151/277 (54%), Gaps = 5/277 (1%) Query: 12 LLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVTT 71 L++ P L+ + ++G P + ++ S +D + FVG AN+ +++ F R+L Sbjct: 19 LMLAPALIYIALLLGIPFLLSIYYSLSDITVGTRAMHFVGLANFQRIVQNPTFWRSLGNA 78 Query: 72 TWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEYG 131 F ++S A +VL + AL L + FRG+ +R L++LPW P + + W I++P Y Sbjct: 79 LVFTLVSQALVVVLAKILALALLRDFRGKWLVRLLILLPWVAPISLGSIGWLWIFDPVYS 138 Query: 132 ALNAALTQLGLL--DSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITA 189 +N L LGL ++ WLG+P A+A++I+ D W+ PL +I LA L +P+DI Sbjct: 139 IINWTLRALGLFGPQTWPVWLGQPDLAMASVILVDVWRLLPLATVIILAGLHGIPQDIHD 198 Query: 190 ASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSI 249 A+ +DGAG + + +P + +LVAL+ + II+V+TRGGP ++T+ L+ Sbjct: 199 AAAMDGAGFWRHLLRINIPLVMPIMLVALLFGIVFTLTDMIIIFVLTRGGPYDTTQVLAS 258 Query: 250 LVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALL 286 L + F+ + G A A I L +L A A LL Sbjct: 259 LAF---FTGIQGGDLAEGAAISLFLFPLLVAVVALLL 292 Lambda K H 0.326 0.138 0.417 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: 295 Number of extensions: 14 Number of successful extensions: 2 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: 293 Length of database: 301 Length adjustment: 26 Effective length of query: 267 Effective length of database: 275 Effective search space: 73425 Effective search space used: 73425 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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