Align ABC transporter for D-Trehalose, permease component 1 (characterized)
to candidate Pf1N1B4_5113 Maltose/maltodextrin ABC transporter, permease protein MalF
Query= reanno::Smeli:SM_b20326 (328 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5113 Length = 295 Score = 379 bits (973), Expect = e-110 Identities = 181/296 (61%), Positives = 233/296 (78%), Gaps = 5/296 (1%) Query: 28 VRSAWLFLAPTFLVLALVAGWPLIRTIYFSFTNASLTNLSGAEFVGFANYLSWITLKSGR 87 VR+AWLFL P L LALVA WPL+RT +FS T+A+L + G F+GF NYL +G Sbjct: 1 VRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYL----FHNGS 56 Query: 88 TIYRGLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQFPGRGLVRAAILIPWA 147 + + G+L DP WWNAV NTL FTV+SV +E LGL+VAL+LN +F GR LVRA ILIPWA Sbjct: 57 S-WSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWA 115 Query: 148 IPTIVSAKMWAWMLNDQFGILNDMLIGLGLIGEKIAWTASPDTAMIAELIVDVWKTTPFM 207 IPTIVSAK+W+WMLNDQFGI+N +++ LGLI +AWTA D +M A +IVDVWKT PF+ Sbjct: 116 IPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFV 175 Query: 208 ALLILAGLQMVPGDIYEAAKIDGVHPVRVFWRVTLPLIRPALMVAVIFRMLDALRIFDLI 267 LL+LA LQM+P D YEAA++DG+HP++VFWRVTLPL+ PAL+VA IFR+LD+LR+FD+I Sbjct: 176 TLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVI 235 Query: 268 YVLTPNNAQTKTMSVMARENLFDFDKFAYGAAASTMLFLIIATITILYMWLGRLNL 323 YVLT N++ T +MSV AR++L +F YG+AAST+LFL++A I +LY++LGR L Sbjct: 236 YVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRRQL 291 Lambda K H 0.328 0.140 0.438 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: 416 Number of extensions: 12 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: 328 Length of database: 295 Length adjustment: 27 Effective length of query: 301 Effective length of database: 268 Effective search space: 80668 Effective search space used: 80668 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