Align Tagatose-6-phosphate kinase; EC 2.7.1.144; Phosphotagatokinase (uncharacterized)
to candidate GFF3290 Psest_3354 1-phosphofructokinase
Query= curated2:Q8XNK5 (310 letters) >FitnessBrowser__psRCH2:GFF3290 Length = 312 Score = 140 bits (353), Expect = 4e-38 Identities = 92/280 (32%), Positives = 143/280 (51%), Gaps = 4/280 (1%) Query: 2 ILTITMNPSIDISYPLDVLNLDSVNRVTKVTKTAGGKGLNVTRVLKQLDADVLASGLLGG 61 +LT+T+NP++D++ L L L VNR + A GKGLNV +VL L + +G LG Sbjct: 4 VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGFLGE 63 Query: 62 FFGDFIKNDLNINGIKHSFSDISGETRNCIAILH-EGNQTEILESGPNISEKEANNFLRH 120 + + G F ++GETR+ + + +G T+I G +SE + L Sbjct: 64 GNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAELLAR 123 Query: 121 FELLVDKANIISISGSLPLGISKDFYVKMLSICNKKDKRVVLDCSGEELRQVLKNDSKPF 180 + LV ++ ++GSLP GI ++V++L+ RV LD SG LR L ++P+ Sbjct: 124 LKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLA--TRPW 181 Query: 181 AIKPNIDELSDLLGVKVKDSIEDLKLILNTPMFNGIEWIVISMGAKGSFAKHNDKFYRVI 240 IKPN +EL++ G+++ S L GIE +V+S GA G Sbjct: 182 LIKPNEEELAEARGIELSGS-SALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS 240 Query: 241 IPKIQVVNPVGSGDSTIAGLTKGLNDGETDENVLKIANTL 280 PK++VV+ VG+GDS +AG+ GL +G E L A + Sbjct: 241 PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAI 280 Lambda K H 0.317 0.137 0.385 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: 175 Number of extensions: 8 Number of successful extensions: 5 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: 310 Length of database: 312 Length adjustment: 27 Effective length of query: 283 Effective length of database: 285 Effective search space: 80655 Effective search space used: 80655 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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