Align Galactofuranose-binding protein YtfQ (characterized)
to candidate Ac3H11_611 Putative sugar ABC transport system, periplasmic binding protein YtfQ precursor
Query= SwissProt::P39325 (318 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_611 Length = 322 Score = 307 bits (787), Expect = 2e-88 Identities = 169/316 (53%), Positives = 223/316 (70%), Gaps = 15/316 (4%) Query: 11 VSAAMSSMALAA----------PLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIAD 60 V+AA++S+ +AA PL +GFSQVG+ES WR A T KS A++ GI LK +D Sbjct: 9 VAAALASVPVAALLPSTAWAQKPLVLGFSQVGAESEWRTANTESIKSAAKEAGIELKFSD 68 Query: 61 GQQKQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKDKS 120 QQKQENQIKA+RSF+AQ VD I +PVV +GWEPVL+EAK A+IPV L DR+++ KD S Sbjct: 69 AQQKQENQIKAIRSFIAQKVDVIAFSPVVESGWEPVLREAKAAKIPVVLTDRAVNTKDTS 128 Query: 121 LYMTTVTADNILEGKLIGDWLVKEVNGK--PCNVVELQGTVGASVAIDRKKGFAEAIKNA 178 LY+T + +D + EG+ G WLV+++ + N+VELQGTVG++ AIDRKKGF E IK Sbjct: 129 LYVTFMGSDFVEEGRKAGRWLVEKMKDQKGEVNIVELQGTVGSAPAIDRKKGFEEIIKAD 188 Query: 179 PNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKP 238 P KIIRSQ+GDFTR+KGKEVME+F+KAE GK I ++YAHNDDM IGAIQAI+EAG+KP Sbjct: 189 PKFKIIRSQTGDFTRAKGKEVMEAFLKAE--GKKINVLYAHNDDMAIGAIQAIEEAGMKP 246 Query: 239 GKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKLTLTKS 298 KDI+ SID V ++AM+ G+ N SVE +P + GP A K K G K +T+ Sbjct: 247 AKDIVIISIDAVKGAFEAMIAGKLNVSVECSP-LLGPQLMAAVKDIKAGKAVPKRIVTEE 305 Query: 299 TLYLPDTAKEELEKKK 314 ++ + A +E+ +K Sbjct: 306 GIFPMEVAAKEMPNRK 321 Lambda K H 0.313 0.130 0.363 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: 308 Number of extensions: 15 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: 318 Length of database: 322 Length adjustment: 28 Effective length of query: 290 Effective length of database: 294 Effective search space: 85260 Effective search space used: 85260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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