Align SmoE, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_106712309.1 CU102_RS17055 sugar ABC transporter substrate-binding protein
Query= TCDB::O30831 (436 letters) >NCBI__GCF_003010955.1:WP_106712309.1 Length = 436 Score = 640 bits (1651), Expect = 0.0 Identities = 305/430 (70%), Positives = 356/430 (82%), Gaps = 1/430 (0%) Query: 8 LMGACAVAALSSAAGAETITVATVNNGDMIRMQGLMSEFNAQHPDITVEWVTLEENVLRQ 67 L+GA + AL AA AET+T+ATVNN DMIRMQ L +F ++PDI +EWVTLEENVLRQ Sbjct: 7 LLGAVSALALGGAAHAETLTIATVNNSDMIRMQKLTEDFTKKNPDIQLEWVTLEENVLRQ 66 Query: 68 KVTTDIATKGGQFDVLTIGTYEVPIWGKQGWLVSLNDLPPEYDADDILPAIRNGLTVDGE 127 +VTTDIATK GQ+D++TIGTYEVPIW KQGWL+ L+ L YD D+LPAI + ++VDG+ Sbjct: 67 RVTTDIATKAGQYDIVTIGTYEVPIWAKQGWLLPLDGLGDSYDKADLLPAISDAVSVDGK 126 Query: 128 LYAAPFYGESSMIMYRKDLMEKAGLTMPDAPTWDFVKEAAQKMTDKDAEVYGICLRGKAG 187 LYA+PFYGES+M+MYRKDL EKAG+T+P+ PTWD + EAA+KMTDK E YGICLRGKAG Sbjct: 127 LYASPFYGESAMVMYRKDLAEKAGVTIPEKPTWDQIAEAAKKMTDKSTETYGICLRGKAG 186 Query: 188 WGENMAFLSAMANSYGARWFDENWQPQFDGEAWKATLTDYLDMMTNYGPPGASKNGFNEN 247 WGENMA L+A ANSYGARWFDE W PQFD WK L Y+D+M GPPGAS NGFNEN Sbjct: 187 WGENMALLTATANSYGARWFDEKWTPQFDQPEWKKALQFYVDLMKEAGPPGASSNGFNEN 246 Query: 248 LALFQQGKCGMWIDATVAASFVTNPEESTVADKVGFALAPDTGKGKRANWLGAWNLAIPA 307 LALFQ GKCG+WIDATVAASFVTNP+ES VAD+VG+AL P G NWL AWNL +PA Sbjct: 247 LALFQTGKCGIWIDATVAASFVTNPKESKVADQVGYALFPTGGVENHGNWLWAWNLGVPA 306 Query: 308 GSQKVDAAKQFIAWATSKDYAELVASKEGWANVPPGTRTSLYENPEYQK-VPFAKMTLDS 366 G+QK +AA++F++WAT K Y+ELVASKEGWANVPPGTR SLY NPEY+K PFAK+TLD+ Sbjct: 307 GTQKAEAAQKFVSWATDKAYSELVASKEGWANVPPGTRKSLYANPEYEKAAPFAKITLDA 366 Query: 367 INAADPTHPAVDPVPYVGVQFVAIPEFQGIGTAVGQQFSAALAGSMSAEQALQAAQQFTT 426 +NAAD + P V PVPY G QFVAIPEFQGIGTAVGQQFSAALAGS+S +QALQ+AQQ TT Sbjct: 367 MNAADTSKPTVKPVPYTGGQFVAIPEFQGIGTAVGQQFSAALAGSVSVDQALQSAQQLTT 426 Query: 427 REMTRAGYIK 436 REMT+ GYIK Sbjct: 427 REMTKGGYIK 436 Lambda K H 0.316 0.131 0.400 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: 743 Number of extensions: 31 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: 436 Length of database: 436 Length adjustment: 32 Effective length of query: 404 Effective length of database: 404 Effective search space: 163216 Effective search space used: 163216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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