Align ABC transporter for L-Histidine, permease component (characterized)
to candidate SMc02738 SMc02738 glycine betaine transport system permease ABC transporter protein
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Smeli:SMc02738 Length = 281 Score = 228 bits (581), Expect = 1e-64 Identities = 122/262 (46%), Positives = 174/262 (66%), Gaps = 2/262 (0%) Query: 10 IADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRK 69 I W +VD L TN+ F +++ L I L +L+ +++A+V +AW R Sbjct: 11 IGAWAKSFVDWLTTNFNLFFDQLANVLSAIISVLLYILQTPHPLIIIAVVTALAWWFRRS 70 Query: 70 V-LATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLM 128 + +A +GLL +V G W + +TLAL+L AT +S+ +G+P GI +AR + S++ Sbjct: 71 LGIAAFTCLGLLLIVNQ-GYWQETTETLALVLAATFVSMAVGVPFGIAAARRAWIYSIMR 129 Query: 129 PLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAI 188 P+LD+MQT+P+FVYLIP L+LFGLG VP + ATVI+A P IRLT LGI ++EA Sbjct: 130 PILDLMQTIPTFVYLIPALILFGLGVVPGLIATVIFAIPAPIRLTRLGIISTPPALVEAA 189 Query: 189 NAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTL 248 +FGA WQ L V+LP A+P IMAG+ QT M++LSMVVIA+++GA GLG VL + T+ Sbjct: 190 ESFGATPWQVLRKVELPFAMPQIMAGLTQTIMLSLSMVVIAALVGADGLGVPVLRALNTV 249 Query: 249 NVGRGLEAGLAIVILAVVIDRI 270 N+ RG E+GL IVILA+V+DR+ Sbjct: 250 NIARGFESGLCIVILAIVLDRL 271 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: 275 Number of extensions: 11 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: 281 Length adjustment: 26 Effective length of query: 257 Effective length of database: 255 Effective search space: 65535 Effective search space used: 65535 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