Align ABC transporter for L-Histidine, permease component (characterized)
to candidate H281DRAFT_02451 H281DRAFT_02451 glycine betaine/proline transport system permease protein
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Burk376:H281DRAFT_02451 Length = 300 Score = 253 bits (647), Expect = 3e-72 Identities = 129/267 (48%), Positives = 181/267 (67%), Gaps = 1/267 (0%) Query: 10 IADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRK 69 + WV+ V L+ + F I + +E L+ P W ++A GI Sbjct: 7 LGTWVDHGVHYLLDHDAKTFDSIGKVIEGFAALIEQGLQAVPMWALMAFFVGIGLWRVGW 66 Query: 70 VLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMP 129 A ++ +L + G G WD+++ TL L L +TLIS+L+G+PLGI +A+S + ++ P Sbjct: 67 RFALFTLLAMLLIYGT-GFWDQMVITLGLTLSSTLISLLLGVPLGIWTAKSRTVEMIVRP 125 Query: 130 LLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAIN 189 +LD+MQTMP+FVYLIP MLFGLG+VP I +TVI+A PP +RLT LGI+ V+ E++EA Sbjct: 126 VLDLMQTMPAFVYLIPAAMLFGLGRVPGILSTVIFAMPPAVRLTSLGIKHVNREIVEAGQ 185 Query: 190 AFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLN 249 AFG WQ L+ VQ P ALPSIM G+NQT MMALSMV+IASM+GA GLG DVL IQ L+ Sbjct: 186 AFGCTPWQLLYKVQFPNALPSIMTGVNQTIMMALSMVIIASMVGAGGLGNDVLASIQRLD 245 Query: 250 VGRGLEAGLAIVILAVVIDRITQAYGR 276 +G G E+GL++V+LA+++DRIT+++GR Sbjct: 246 IGLGFESGLSVVMLAIILDRITESFGR 272 Lambda K H 0.328 0.142 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: 284 Number of extensions: 10 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: 283 Length of database: 300 Length adjustment: 26 Effective length of query: 257 Effective length of database: 274 Effective search space: 70418 Effective search space used: 70418 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