Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate WP_035236484.1 Q366_RS03740 glycine/betaine ABC transporter permease
Query= SwissProt::P14176 (354 letters) >NCBI__GCF_000745975.1:WP_035236484.1 Length = 276 Score = 303 bits (777), Expect = 3e-87 Identities = 144/271 (53%), Positives = 207/271 (76%) Query: 57 FHKTLIPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALI 116 F + ++P+D W+T +DW+V ++R +FQ ++ PV+ IL GF L +P + I + A Sbjct: 2 FGEKVLPIDIWITAFVDWLVNNYRDIFQMIKWPVEQILTGFDIGLNAVPPIIIIGILAFC 61 Query: 117 AWQISGVGMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRA 176 AW+ SG G+ V ++V+++ IG IG W+ M TLA+VL ++LF ++G+P+GI RS R Sbjct: 62 AWRFSGWGLAVFSVVAMVFIGLIGFWADTMTTLAMVLASVLFSTLVGVPVGIAAGRSDRV 121 Query: 177 AKIIRPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPAD 236 I+RP LDAMQTTP+FVYLVPIVMLF +GNV GV+ TIIFA+PPI+RLT LGI V + Sbjct: 122 ETIVRPFLDAMQTTPSFVYLVPIVMLFSVGNVAGVLATIIFAMPPIVRLTSLGIRGVHPE 181 Query: 237 LIEASRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLR 296 L+EA+ +FGA+ Q+LFKVQ+PLAMPTI+AG+NQT+M+AL+MVVIA++I GGLG V++ Sbjct: 182 LVEAATAFGATRSQVLFKVQIPLAMPTILAGLNQTIMMALAMVVIAALIGAGGLGSPVIQ 241 Query: 297 GIGRLDMGLATVGGVGIVILAIILDRLTQAV 327 G+ LD+GLA + G+ IV+LA++LDR+TQ++ Sbjct: 242 GLNTLDIGLAVMAGLSIVLLAVVLDRITQSM 272 Lambda K H 0.326 0.141 0.435 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: 317 Number of extensions: 13 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: 354 Length of database: 276 Length adjustment: 27 Effective length of query: 327 Effective length of database: 249 Effective search space: 81423 Effective search space used: 81423 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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