Align ABC transporter for L-Histidine, permease component (characterized)
to candidate GFF3324 PGA1_c33770 putative ABC transporter permease protein
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Phaeo:GFF3324 Length = 516 Score = 218 bits (554), Expect = 3e-61 Identities = 114/260 (43%), Positives = 167/260 (64%), Gaps = 1/260 (0%) Query: 13 WVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRKVLA 72 WV ++ V N F ++ + + LE +L PW ++ +++ + W T + A Sbjct: 254 WVEDFIAWCVRNSETFFDWLTFGIRALLDALEVILVQTPWIVIASLIVLLTW-LTAGIRA 312 Query: 73 TAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLD 132 L +G +G W+ M TLAL+ A +S+LIGIPLG+ +AR R + + P++D Sbjct: 313 AIYSGAFLAYMGLLGFWEGAMTTLALLGTAACLSILIGIPLGMFAARRPRFYAFIQPIMD 372 Query: 133 IMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFG 192 MQTMP+FV+++PV+ FG+GK A+ T+I+ P++RLT LG+R V V EA +FG Sbjct: 373 FMQTMPAFVFMVPVIAFFGVGKPAAVVVTMIFGGTPVVRLTVLGLRGVPESVREAAISFG 432 Query: 193 ANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGR 252 AN+W L V LPLA PSI AGINQT M++L+MVV+AS+IGA+GLGEDVL +Q NVG+ Sbjct: 433 ANKWYLLTKVDLPLASPSIRAGINQTIMLSLAMVVVASLIGAKGLGEDVLEALQYANVGQ 492 Query: 253 GLEAGLAIVILAVVIDRITQ 272 G+ AG AI+ A+++DRI Q Sbjct: 493 GILAGFAILFCAMILDRIVQ 512 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: 394 Number of extensions: 18 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: 516 Length adjustment: 30 Effective length of query: 253 Effective length of database: 486 Effective search space: 122958 Effective search space used: 122958 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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