Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate 8499892 DvMF_0657 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Miya:8499892 Length = 297 Score = 153 bits (387), Expect = 4e-42 Identities = 90/268 (33%), Positives = 138/268 (51%), Gaps = 2/268 (0%) Query: 4 TWISTRAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSN 63 T + AWLL+LP L + A +P V+T SF G FVG +Y +L Sbjct: 10 TMRTIHAWLLLLPALAFIAAFTHYPAVNTFIHSFFLDGRGGAPAQFVGLEHYQYLLEDEV 69 Query: 64 FQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWR 123 F++ALV FA ++ + L + A L+N G++ LR +P LP + A +W Sbjct: 70 FRKALVNNLLFASGTIPLSIGLAMTMAFLVNAGLAGQSVLRLCYFVPTVLPMIAVANIWL 129 Query: 124 LIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAV 183 Y PEYG L LGL +WLG TAL +I WK+ + LAALQ + Sbjct: 130 FFYTPEYGLLEQIRGALGLAGV--NWLGSESTALPCVIAVAVWKDAGFFMIFYLAALQQI 187 Query: 184 PRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANS 243 P + A++++GA +R V++P L L LV TI AF++ D ++V+T+GGP N+ Sbjct: 188 PPSLGEAAMLEGASRLYYYRRVVIPLLMPTTLFVLVNATINAFRMVDHLFVLTQGGPNNA 247 Query: 244 TRTLSILVYQEAFSFQRAGSGASLALIV 271 + L +Y+ +F + G GA+L +++ Sbjct: 248 SSLLLYYIYEVSFKYWDTGYGAALTMVL 275 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: 224 Number of extensions: 12 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: 293 Length of database: 297 Length adjustment: 26 Effective length of query: 267 Effective length of database: 271 Effective search space: 72357 Effective search space used: 72357 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