Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_062736445.1 AYX06_RS14980 sugar porter family MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >NCBI__GCF_001580365.1:WP_062736445.1 Length = 482 Score = 655 bits (1690), Expect = 0.0 Identities = 329/470 (70%), Positives = 393/470 (83%), Gaps = 2/470 (0%) Query: 12 EKSKKLPPLTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVV 71 E + LPPLT GP+RKRL +++VA FGGLLFGYDTGVINGAL PM+ ELGLT FTEGVV Sbjct: 8 ETAAALPPLTSGPHRKRLGLISIVACFGGLLFGYDTGVINGALRPMSEELGLTPFTEGVV 67 Query: 72 TSSLLFGAAAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGL 131 TSSL+F AA GA+ GRISD WGRR+TI+ L+V FFVGTMI VF PS+ V+V GRV LGL Sbjct: 68 TSSLVFAAAVGALSGGRISDAWGRRRTILLLSVLFFVGTMIVVFTPSYEVLVAGRVCLGL 127 Query: 132 AVGGASTVVPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRY 191 AVGGAS VVPV+LAELAP+EIRGS+AGRNE+ IV+GQL+AFVINAIIGNVF VWR Sbjct: 128 AVGGASAVVPVFLAELAPYEIRGSIAGRNEVAIVIGQLSAFVINAIIGNVFSESPSVWRV 187 Query: 192 MLAIAAIPAIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAR 251 M AI+A+PA+ALF GMLR+PESPRWLVE+GR EA VL+T+R ERA AE+ +VEH+A Sbjct: 188 MFAISALPAVALFIGMLRMPESPRWLVEKGRHREALEVLKTVRSEERAIAELGEVEHVAE 247 Query: 252 EEHAVSEKSMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENA 311 EE A E +GL ILS+K L+RILLVGIGLG+AQQLTGINSIMYYGQ+VLIE+GFS NA Sbjct: 248 EERA--EHQIGLAAILSNKNLIRILLVGIGLGIAQQLTGINSIMYYGQIVLIESGFSANA 305 Query: 312 ALIANVAPGVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLR 371 ALIAN+APGVIAVVG FIAL++MDR++RR T + G +LTT H+LIG +S+ G+PLR Sbjct: 306 ALIANIAPGVIAVVGGFIALYLMDRLDRRKTFMIGLTLTTTCHLLIGASSMLLEEGNPLR 365 Query: 372 PYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPT 431 P+VIL LVV FVGSMQTFLNVA WV LSE+FPL MRG IG+SVF LW+AN L L+FP+ Sbjct: 366 PFVILALVVAFVGSMQTFLNVAVWVYLSEVFPLHMRGVGIGVSVFMLWVANGVLSLYFPS 425 Query: 432 IMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEIDEDVTSGVIF 481 ++ AVG+TGTFF+FAG+G +AL+F+YTQVPETRGRTLE ++EDVT+G I+ Sbjct: 426 LVAAVGITGTFFLFAGVGALALLFVYTQVPETRGRTLEALEEDVTTGAIY 475 Lambda K H 0.327 0.142 0.420 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: 756 Number of extensions: 29 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: 491 Length of database: 482 Length adjustment: 34 Effective length of query: 457 Effective length of database: 448 Effective search space: 204736 Effective search space used: 204736 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: 52 (24.6 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