Align Inositol transport system permease protein (characterized)
to candidate H281DRAFT_04461 H281DRAFT_04461 monosaccharide ABC transporter membrane protein, CUT2 family
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Burk376:H281DRAFT_04461 Length = 390 Score = 387 bits (995), Expect = e-112 Identities = 204/364 (56%), Positives = 250/364 (68%), Gaps = 5/364 (1%) Query: 5 PTQFAEDERIKTRSKFREAMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQIS 64 P DER++ S F + RPE I G + VF +F + AG SGMFN GVMNWSQ+S Sbjct: 26 PETDGRDERVRKESWFGHLLNRPEFAAISGAVLVFLVFALTAGGSGMFNLDGVMNWSQVS 85 Query: 65 AQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIG 124 A I++VGACLLMIAGEFDLS+GSMIGFAGM++AI +V WP+ LAIL F + +G Sbjct: 86 AYLGILSVGACLLMIAGEFDLSIGSMIGFAGMMVAIPTVYFHWPISLAILFAFVGSMLLG 145 Query: 125 ALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLA-ALFG 183 ALNG++V+RT LPSFIVTLAFLFILRG + L +TI+ GV D A+ DWLA LF Sbjct: 146 ALNGYLVMRTRLPSFIVTLAFLFILRGLTLALSIMFADRTIVSGVGDLAQQDWLANTLFH 205 Query: 184 GKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNW 243 G L GLF +G + + G +V G+P +I+W L I +L KTR GNW Sbjct: 206 GVALQGLFTMLAHHGIGTLLD----NGHALVPGIPKVILWWFGLAAICAFVLAKTRAGNW 261 Query: 244 IFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAI 303 I A GGDA AA+N G+PV RVKIL+F+ TAFC+ +FA QV + G A +DRGL KEFEAI Sbjct: 262 ILAVGGDANAAKNVGIPVRRVKILLFVLTAFCSCLFAVLQVCDIGSAAADRGLQKEFEAI 321 Query: 304 IAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNT 363 IA VIGG LLTGGYGSV+GA GALIFGVVQ G+ + V S FRVFLG++LL AV+ N Sbjct: 322 IAAVIGGTLLTGGYGSVIGACFGALIFGVVQIGITYTNVSSDWFRVFLGVMLLIAVLFNH 381 Query: 364 YIRR 367 Y+RR Sbjct: 382 YVRR 385 Lambda K H 0.330 0.145 0.443 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: 546 Number of extensions: 29 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: 373 Length of database: 390 Length adjustment: 30 Effective length of query: 343 Effective length of database: 360 Effective search space: 123480 Effective search space used: 123480 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 (21.8 bits) S2: 50 (23.9 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