Align SmoE, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate Ac3H11_2944 Various polyols ABC transporter, periplasmic substrate-binding protein
Query= TCDB::O30831 (436 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2944 Length = 443 Score = 534 bits (1375), Expect = e-156 Identities = 260/435 (59%), Positives = 324/435 (74%), Gaps = 5/435 (1%) Query: 6 RALMGACAVAA--LSSAAGAET-ITVATVNNGDMIRMQGLMSEFNAQHPDITVEWVTLEE 62 R + A A+AA +AA A+T + +ATVNNG MI MQ L F HPDI ++WVTLEE Sbjct: 10 RLALAAAALAASLCGAAAHAQTELVIATVNNGHMIEMQKLSKNFEQAHPDIKLKWVTLEE 69 Query: 63 NVLRQKVTTDIATKGGQFDVLTIGTYEVPIWGKQGWLVSLNDLPPEYDADDILPAIRNGL 122 VLRQ+VTTDIATKGGQFDV+TIG YE PIWGK+GWL L YD DD+LPA+RNGL Sbjct: 70 GVLRQRVTTDIATKGGQFDVMTIGMYEAPIWGKKGWLQELKT-DAAYDVDDLLPAVRNGL 128 Query: 123 TVDGELYAAPFYGESSMIMYRKDLMEKAGLTMPDAPTWDFVKEAAQKMTDKDAEVYGICL 182 ++DG+L+AAPFYGESSM+MYRKDL +KAG+ +P+ PTW +K+ A K+ D VYGICL Sbjct: 129 SIDGKLFAAPFYGESSMLMYRKDLADKAGVQVPERPTWPQIKDLAAKIHDPKNGVYGICL 188 Query: 183 RGKAGWGENMAFLSAMANSYGARWFDENWQPQFDGEAWKATLTDYLDMMTNYGPPGASKN 242 RGK GWG+NMAFLS + N++G +WFD W+PQ + + WK +T Y+D++ NYGPPG+S N Sbjct: 189 RGKPGWGDNMAFLSTLVNTFGGQWFDMQWKPQLESKPWKEAITFYVDLLKNYGPPGSSAN 248 Query: 243 GFNENLALFQQGKCGMWIDATVAASFVTNPEESTVADKVGFALAPDTGKGKRANWLGAWN 302 FNE LAL GKCGMWIDAT+AASFV++P++S VAD++ FA AP K ANWL +WN Sbjct: 249 SFNEILALTNSGKCGMWIDATIAASFVSDPKQSKVADQMAFAQAPTMNTPKGANWLWSWN 308 Query: 303 LAIPAGSQKVDAAKQFIAWATSKDYAELVASKEGWANVPPGTRTSLYENPEYQKVP-FAK 361 LAIPAGS+KVDAA++FI W+TSK+Y +LVA GWANVP GTR S Y +PE+QK FA Sbjct: 309 LAIPAGSKKVDAAQKFITWSTSKEYVQLVAKTNGWANVPTGTRKSTYASPEFQKAARFAA 368 Query: 362 MTLDSINAADPTHPAVDPVPYVGVQFVAIPEFQGIGTAVGQQFSAALAGSMSAEQALQAA 421 +I++A+PT + PYVGVQF AIPEFQ IG AVGQQ SAALAG + + AL+A+ Sbjct: 369 AEKVAIDSANPTDSTLPKSPYVGVQFAAIPEFQAIGIAVGQQMSAALAGKTTVDAALKAS 428 Query: 422 QQFTTREMTRAGYIK 436 Q REM +AGY K Sbjct: 429 QVSADREMKKAGYYK 443 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: 638 Number of extensions: 17 Number of successful extensions: 3 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: 443 Length adjustment: 32 Effective length of query: 404 Effective length of database: 411 Effective search space: 166044 Effective search space used: 166044 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 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