Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 158 bits (400), Expect = 1e-43 Identities = 97/288 (33%), Positives = 149/288 (51%), Gaps = 7/288 (2%) Query: 10 AWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEG----GFVGTANYIKMLGGSNFQ 65 AWL + P L+V+ P++ + LS TD L FV NY ++L F Sbjct: 7 AWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPLFW 66 Query: 66 RALVTTTWFAVISVAAEMVLGVLAALLLNQQF-RGRTALRALMILPWALPTVVNATLWRL 124 AL T +F ++ V +V + AALLLN R + R + P V A +WR Sbjct: 67 SALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWRY 126 Query: 125 IYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVP 184 ++N +YG N AL LG+ WLG+P A+ +I+ WKNF +I LAALQA+P Sbjct: 127 LFNTKYGLANYALGGLGIHPV--DWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQAIP 184 Query: 185 RDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANST 244 D+ A+ +DGA P +FR + +P L LL+ +L F++F +VMT GGP ST Sbjct: 185 ADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGPLQST 244 Query: 245 RTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRKAAGA 292 ++ L+Y+E F + GS +++A ++ L++ + A + R+ A Sbjct: 245 TSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLRVARRGGEA 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: 233 Number of extensions: 16 Number of successful extensions: 5 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: 292 Length adjustment: 26 Effective length of query: 267 Effective length of database: 266 Effective search space: 71022 Effective search space used: 71022 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