Align Galactofuranose-binding protein YtfQ (characterized)
to candidate HSERO_RS05170 HSERO_RS05170 LacI family transcription regulator
Query= SwissProt::P39325 (318 letters) >FitnessBrowser__HerbieS:HSERO_RS05170 Length = 324 Score = 315 bits (806), Expect = 1e-90 Identities = 170/314 (54%), Positives = 222/314 (70%), Gaps = 8/314 (2%) Query: 6 LIVSAVSAAMSSMALAA--PLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIADGQQ 63 + +S S+AMS A AA PLT+GFSQVG+ES WR A T K A++ G+ LK AD QQ Sbjct: 13 ICLSLGSSAMSLPAFAADKPLTMGFSQVGAESEWRTANTVSIKDAAKQAGVNLKFADAQQ 72 Query: 64 KQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKDKSLYM 123 KQENQ+KA+RSF+AQ VD I +PVV +GWE VL+EAK A+IPV L DR+++V DKSLY+ Sbjct: 73 KQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKSLYV 132 Query: 124 TTVTADNILEGKLIGDWLVKEVNGKPC---NVVELQGTVGASVAIDRKKGFAEAIKNAPN 180 T + +D + EG+ G WL+++ P N+VELQGTVG++ AIDRK GF E IK P Sbjct: 133 TFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKGEPR 192 Query: 181 IKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKPGK 240 +KIIRSQ+GDFTR+KGKEVME+F+KAE GK I ++YAHNDDM IGAIQAI+EAG+KPGK Sbjct: 193 LKIIRSQTGDFTRAKGKEVMEAFLKAE--GKKINVLYAHNDDMAIGAIQAIEEAGMKPGK 250 Query: 241 DILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKLTLTKSTL 300 DI+ SIDGV ++AMM G+ N +VE +P + GP + K K G K T+ + Sbjct: 251 DIIIISIDGVKGAFEAMMAGKLNVTVECSP-LLGPQLMQIAKDIKAGKEVPKRITTEEGI 309 Query: 301 YLPDTAKEELEKKK 314 + + A +E +K Sbjct: 310 FPAEVAAKEFPNRK 323 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: 314 Number of extensions: 12 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: 324 Length adjustment: 28 Effective length of query: 290 Effective length of database: 296 Effective search space: 85840 Effective search space used: 85840 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