Align PTS system glucitol/sorbitol-specific EIIB component; EII-Gut; Enzyme II-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIB component; EC 2.7.1.198 (characterized)
to candidate WP_010631559.1 RH97_RS06580 PTS sorbitol transporter subunit IIB
Query= SwissProt::O32333 (336 letters) >NCBI__GCF_000246965.1:WP_010631559.1 Length = 338 Score = 457 bits (1177), Expect = e-133 Identities = 224/339 (66%), Positives = 276/339 (81%), Gaps = 7/339 (2%) Query: 1 MEKYNAIKIVKGSGGFGGPLTVKPEEGKDTLLYITGGGAEPEIVEKIVNLTGCKAVNGFK 60 M +Y + K+V+G GGFGGPL + P EGKD ++YI GGG P IV+K+V LTG VNGFK Sbjct: 1 MTEYKSAKVVRGHGGFGGPLIITPREGKDKIVYIVGGGNRPAIVDKLVELTGGVPVNGFK 60 Query: 61 TSVPEEQIFLVIIDCGGTLRCGIYPQKRIPTINVMPVGKSGPLAKFITEDIYVSAVGLNQ 120 TSVP+E+I +IIDCGGTLRCGIYP+K IPTINVMP GKSGPLA++ITE IYVS V ++Q Sbjct: 61 TSVPDEKIAAIIIDCGGTLRCGIYPKKGIPTINVMPTGKSGPLAQYITEKIYVSNVTVDQ 120 Query: 121 ISLADSSAEPIKSTKVPEEG----KREFKYSADKKVSQSLAENSKSSIVQKIGMGAGKVV 176 IS A A P + + G +R+FKYS DK +S++ A + + S++ +IG+GAGKV+ Sbjct: 121 ISAA---AGPASNESEQDAGAGAQQRQFKYSTDKTISKTKAASDQQSVLTRIGLGAGKVI 177 Query: 177 NTLYQAGRDAVQSMITTILPFMAFVAMLIGIIQGSGFGNWFAKILVPLAGNGIGLMILGF 236 +T YQAGRD++Q+M+TTILPFMAFVAMLIG+IQGSG G FAKI+ PLAGN GL+++GF Sbjct: 178 DTFYQAGRDSIQTMLTTILPFMAFVAMLIGVIQGSGIGTLFAKIMTPLAGNIWGLLLIGF 237 Query: 237 ICSIPLLSALLGPGAVIAQIVGTLIGVEIGKGTIPPSLALPALFAINTQCACDFIPVGLG 296 +CS+P LS LLGPG VIAQI+GTLIGV+I +G +PP LALPALFAINTQ ACDF+PVGLG Sbjct: 238 VCSLPFLSPLLGPGGVIAQIIGTLIGVQIAQGNVPPQLALPALFAINTQNACDFVPVGLG 297 Query: 297 LAEAEPETVEVGVPSVLYSRFMIGVPRVAVAWVASIGLY 335 LAEA+PETVEVGVPSVLYSRF+ GVPRVA+AW+ S GLY Sbjct: 298 LAEAKPETVEVGVPSVLYSRFLTGVPRVALAWLCSFGLY 336 Lambda K H 0.319 0.139 0.405 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: 537 Number of extensions: 25 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: 336 Length of database: 338 Length adjustment: 28 Effective length of query: 308 Effective length of database: 310 Effective search space: 95480 Effective search space used: 95480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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