Align ABC transporter for L-Histidine, permease component (characterized)
to candidate 8500288 DvMF_1044 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Miya:8500288 Length = 280 Score = 267 bits (682), Expect = 2e-76 Identities = 142/267 (53%), Positives = 185/267 (69%) Query: 10 IADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRK 69 + W+ +D LVT+ R S + LE L P L++A VG +AW TR+ Sbjct: 10 LGQWLEAAIDFLVTHLAPATRAFSAVTESGLNLLEAGLDALPPLLVIAFVGLVAWRVTRQ 69 Query: 70 VLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMP 129 V V L LV +GLW M TLAL+LVATL++VL+GIPLGI +A S+R R+V+MP Sbjct: 70 VALGVFAVAGLALVWNMGLWQATMSTLALVLVATLLAVLVGIPLGIAAAMSDRARAVVMP 129 Query: 130 LLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAIN 189 +LD+MQTMP+FVYLIP + FGLGKV A+FATVI+A PP IR T LGIRQV E++E Sbjct: 130 VLDVMQTMPAFVYLIPAIPFFGLGKVAAVFATVIFAMPPAIRFTCLGIRQVPAELVECAE 189 Query: 190 AFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLN 249 AFG R+Q+L ++LPLA P+++AG+NQT M+ALSMVVIA+MIGARGLG +V IQ L Sbjct: 190 AFGTGRFQRLVKLELPLAAPTMLAGVNQTVMLALSMVVIAAMIGARGLGGEVWKAIQRLE 249 Query: 250 VGRGLEAGLAIVILAVVIDRITQAYGR 276 +G G EAG+ IVI+A+ +DRI Q G+ Sbjct: 250 MGNGFEAGIGIVIVAICLDRILQHVGK 276 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: 303 Number of extensions: 10 Number of successful extensions: 1 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: 280 Length adjustment: 26 Effective length of query: 257 Effective length of database: 254 Effective search space: 65278 Effective search space used: 65278 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