Align tagatose-6-phosphate kinase (EC 2.7.1.144) (characterized)
to candidate BWI76_RS24860 BWI76_RS24860 1-phosphofructokinase
Query= BRENDA::P0A0B9 (310 letters) >FitnessBrowser__Koxy:BWI76_RS24860 Length = 304 Score = 132 bits (331), Expect = 1e-35 Identities = 96/316 (30%), Positives = 159/316 (50%), Gaps = 18/316 (5%) Query: 1 MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIG 60 MI TLTLN ++D++ LK VNR + GKG+NV+ +L +P G G Sbjct: 1 MIHTLTLNTAIDMNIFCDPLKPSAVNRTRHTEYCPNGKGVNVSLILNHYQQPTHIIGIFG 60 Query: 61 GELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKH 120 G G++I ++L IK + TR I I ++ +++ G +ID++ I H Sbjct: 61 GFTGRYIVEELRQKKIKVTPAWVSEPTRINIFINDGAEEYKLVNPGAKIDDECKQQVIHH 120 Query: 121 FEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPT 180 Q + + +AISGSLP G+ +YA+IIE CQ K VILD S L+ +LE +P Sbjct: 121 L-QCVASGDYLAISGSLPPGIESRFYAEIIELCQQKRCEVILDISHPVLRQLLE--LRPL 177 Query: 181 VIKPNISELYQLL------NQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNH 234 +IKPN EL ++ +Q + E++ +L Q G +++++GA+G + Sbjct: 178 LIKPNDDELREIFGLDVSNHQQVREAMRTLHQL-------GARNVLLTMGAEGLYFSDGE 230 Query: 235 TFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVN 294 + + P I++++ +GD+ + S LN E+ L A+ G A A G Sbjct: 231 GVWFCSAPKIALVSSACAGDAALGAFLSKWLNKEDVAHALALASATGADVAGSAGLG--K 288 Query: 295 LNNYDDLFNQIEVLEV 310 L ++L QI+V+++ Sbjct: 289 LQRTEELLQQIQVVQL 304 Lambda K H 0.315 0.135 0.380 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: 270 Number of extensions: 12 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: 310 Length of database: 304 Length adjustment: 27 Effective length of query: 283 Effective length of database: 277 Effective search space: 78391 Effective search space used: 78391 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: 42 (22.0 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