Align Histidine transport system permease protein HisM (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= SwissProt::P0A2I7 (235 letters) >FitnessBrowser__Miya:8500595 Length = 337 Score = 105 bits (261), Expect = 1e-27 Identities = 69/218 (31%), Positives = 116/218 (53%), Gaps = 15/218 (6%) Query: 17 GYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLL 76 G G+ ITL + + +++ G ++ V+ + R+S N +R+ + I RG+PL VQ+ Sbjct: 125 GILLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIF 184 Query: 77 VFYSGMYTLEIVKGTDLLNAFFR-------SGLNCTVLALTLNTCAYTTEIFAGAIRSVP 129 ++Y V GT L+NA S L V+AL L T AY EI I+SV Sbjct: 185 LWY-------FVVGT-LINALLEHVGLGGISPLWYGVMALALFTGAYVAEIVRAGIQSVH 236 Query: 130 HGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIA 189 G++EAAR+ G + + R +ILP A R +P + + I ++ ++L + +L K Sbjct: 237 RGQMEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRELTKAT 296 Query: 190 RDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAERR 227 R++ + + QPF + + AVLYL++++ L + ERR Sbjct: 297 REVVTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334 Lambda K H 0.330 0.141 0.429 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: 215 Number of extensions: 8 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: 235 Length of database: 337 Length adjustment: 26 Effective length of query: 209 Effective length of database: 311 Effective search space: 64999 Effective search space used: 64999 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 (21.9 bits) S2: 47 (22.7 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