Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate HSERO_RS20095 HSERO_RS20095 ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__HerbieS:HSERO_RS20095 Length = 316 Score = 127 bits (320), Expect = 3e-34 Identities = 82/271 (30%), Positives = 138/271 (50%), Gaps = 9/271 (3%) Query: 56 LLALGIMLSMVSGNGGIDLSGVGLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMM 115 L+ LG ML + +G G IDLS L+G + R + G+D +L L + L + Sbjct: 52 LVGLGQMLVVTTGPGNIDLSIPSTIALAGALGL----RTMGGEDGGIL---LGLVVTLGV 104 Query: 116 GLLGGLLNGVVIARLRLTPILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVL 175 G+ GL N ++I L++ PI+ T+ + + A+ + G + + L+ G +L Sbjct: 105 GVGIGLANYLLIRLLQIPPIIATMSSSFILQSLAIHVGQGLKITPPQL--LASFATGWLL 162 Query: 176 QVPIAFCIFLAAVIVLGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVL 235 VP + LA + L W+L R+ FG L +G N +AA+ AGI R+ Y +C V Sbjct: 163 HVPQLAWLVLAVALGLAWILGRTLFGRFLSAVGQNARAAWLAGIGVERIRCLCYVLCAVF 222 Query: 236 ASLAGLISATHTSSAKWDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSS 295 A+L L+ A + A D GN YLL+++ + V+GG + GG + ++ AA L F ++ Sbjct: 223 AALCALLIAGFSGGASLDMGNEYLLMSVAVVVIGGTSVTGGRPSVAGIWGAALFLYFTNT 282 Query: 296 LFNLLGVSQFFGDCAWGFLLLLSLAFAGGER 326 L N++G+S G +++ + +G R Sbjct: 283 LLNVVGLSAGERSVLSGLIIIAVIVCSGRRR 313 Lambda K H 0.327 0.143 0.429 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: 347 Number of extensions: 18 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: 357 Length of database: 316 Length adjustment: 28 Effective length of query: 329 Effective length of database: 288 Effective search space: 94752 Effective search space used: 94752 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: 49 (23.5 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