Align Tagatose-6-phosphate kinase; Phosphotagatokinase; EC 2.7.1.144 (characterized)
to candidate AZOBR_RS30840 AZOBR_RS30840 hypothetical protein
Query= SwissProt::P23391 (310 letters) >FitnessBrowser__azobra:AZOBR_RS30840 Length = 323 Score = 127 bits (320), Expect = 3e-34 Identities = 88/269 (32%), Positives = 140/269 (52%), Gaps = 10/269 (3%) Query: 2 ILTVTLNPSVDISYPLETLKIDTVNRVKDVSKTAGGKGLNVTRVLYESG-----DKVTAT 56 ++TVTLN ++D + + VNR ++TAGGKG+NV L + VTAT Sbjct: 11 VVTVTLNAAIDQTLDVPGFAAGAVNRAVAETRTAGGKGINVAAFLAGASLAGGATPVTAT 70 Query: 57 GFLGGKIGEFIESELEQSPVSPAFYKISGNTRNCIAIL-HEGNQ-TEILEQGPTISHEEA 114 GFLG + ++ + + +++G +R I ++ EG+ T+I G + E Sbjct: 71 GFLGEENTAVFDALFRRRGIRDRCLRLAGRSRVNIKLVDREGHSVTDINLPGLHVPAESW 130 Query: 115 EGFLDHYSNLIKQSEVVTISGSLPSGLPNDYYEKLIQLASDEGVAVVLDCSGAPLETVLK 174 G L +L + +SGS+P+G+P+ Y +++ G VV+D SG PL + Sbjct: 131 RGLLTVVDDLAVTNRTFVLSGSVPAGVPDTAYTEMVTALHRRGAFVVVDASGPPLRHAV- 189 Query: 175 SSAKPTAIKPNNEELSQLLGKEVTKDIEELKDVLKESLFSGIEWIVVSLGRNGAFAKHGD 234 +A+P +KPN EL++LLG+ + KD E+ +E SGI +VVSLG GA G Sbjct: 190 -AARPDMVKPNAAELAELLGRPL-KDRAEVVRAARELSESGIALVVVSLGAEGAVFVEGG 247 Query: 235 VFYKVDIPDIPVVNPVGSGDSTVAGIASA 263 P + V + VG+GD+ VAG+ +A Sbjct: 248 RALLAMPPPVEVASTVGAGDAMVAGVVAA 276 Lambda K H 0.311 0.131 0.361 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: 206 Number of extensions: 7 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: 323 Length adjustment: 27 Effective length of query: 283 Effective length of database: 296 Effective search space: 83768 Effective search space used: 83768 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 (21.8 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