Align ABC transporter for L-Histidine, permease component (characterized)
to candidate 207785 DVU2298 glycine/betaine/L-proline ABC transporter, permease protein
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >MicrobesOnline__882:207785 Length = 283 Score = 256 bits (653), Expect = 5e-73 Identities = 136/273 (49%), Positives = 185/273 (67%), Gaps = 11/273 (4%) Query: 4 ESFTFSIADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIA 63 E+FT ++ +W +G + T G+ I LE LL P W + +V +A Sbjct: 16 EAFTDNMVEWCSGATRAFSTVAGN-----------GIDMLESLLGSIPPWAFIPVVALLA 64 Query: 64 WHATRKVLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRL 123 W ATRK A + L+ +GLW+ M T+AL+LVAT ++V+ G+PLGI +A + + Sbjct: 65 WRATRKPGIGAFALLGFGLIWNLGLWEATMSTIALVLVATALAVVTGVPLGIAAAVNVTV 124 Query: 124 RSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGE 183 R VLMP+LD+MQTMP+FVYLIP + FGLGKV A+FATV++A PP IR T LGIRQV + Sbjct: 125 RKVLMPVLDLMQTMPAFVYLIPAIPFFGLGKVAAVFATVVFAMPPAIRFTCLGIRQVPDD 184 Query: 184 VMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLV 243 ++E AFG +RWQ+L ++LPLA P+I+AG+NQT M+ALSMVVIA+MIGARGLG +V Sbjct: 185 LVECAEAFGTSRWQRLVKLELPLAAPTILAGVNQTIMLALSMVVIAAMIGARGLGGEVWK 244 Query: 244 GIQTLNVGRGLEAGLAIVILAVVIDRITQAYGR 276 IQ L +G G EAG+ IVI+A+ +DR+ Q GR Sbjct: 245 AIQRLELGSGFEAGIGIVIVAICLDRVLQHIGR 277 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: 294 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 283 Length of database: 283 Length adjustment: 26 Effective length of query: 257 Effective length of database: 257 Effective search space: 66049 Effective search space used: 66049 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: 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