Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate HSERO_RS05555 HSERO_RS05555 ABC transporter permease
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >FitnessBrowser__HerbieS:HSERO_RS05555 Length = 618 Score = 209 bits (533), Expect = 1e-58 Identities = 125/413 (30%), Positives = 216/413 (52%), Gaps = 2/413 (0%) Query: 3 LAVFLSSLFGL-MLLGMPIAFALMLTGVALMVHLDFFDAQLVAQNMLSGADNYPLMAVPF 61 L VF + + +LLG+PIAF L VA M+ + +VA G + L+AVP Sbjct: 200 LVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTVTTSPLAVVAGRFDEGMSSLILLAVPL 259 Query: 62 FILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALATL 121 FIL G L+ G+++ +++ SL+GH+RGGL YV +GA ++++ +SG+ AD AA+A + Sbjct: 260 FILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPV 319 Query: 122 LIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGLLM 181 L+P M+ G L+A+ G +A IPPS+ I G SI+ LF GI+PG+++ Sbjct: 320 LLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVL 379 Query: 182 GAGLVITWMFVVRGMTVKLQPKASWGERRTALVEGVWALALPVIIIGGLRGGIFTPTEAA 241 L I + + +Q RT L+ + AL LP++I + G+ T TE + Sbjct: 380 AVLLAILARWRSAEIMEGIQRAPGRVVLRT-LIIALPALLLPILIRTAVVEGVATATEVS 438 Query: 242 VVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVTLADLPQQM 301 + YS+V L VYR+ K L P+LV A + ++F+ A S+ +T + + Sbjct: 439 TIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFSHAL 498 Query: 302 NEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYFGVMF 361 E + + ++ + +G+V++ P +++ P+L P+A A G+ ++ ++ Sbjct: 499 AEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYAMVI 558 Query: 362 VLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVP 414 +L+ +GL PP C + R+ + A + IWP+L ++ L ++ VP Sbjct: 559 ILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVP 611 Lambda K H 0.328 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: 565 Number of extensions: 25 Number of successful extensions: 4 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: 426 Length of database: 618 Length adjustment: 35 Effective length of query: 391 Effective length of database: 583 Effective search space: 227953 Effective search space used: 227953 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: 52 (24.6 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