Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate AO353_05480 AO353_05480 1-phosphofructokinase
Query= reanno::BFirm:BPHYT_RS02045 (305 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05480 Length = 313 Score = 49.3 bits (116), Expect = 1e-10 Identities = 71/269 (26%), Positives = 105/269 (39%), Gaps = 43/269 (15%) Query: 37 GAGWNVARCVARLGLPTACAGSLGVDNFSDELWNASVAAGLDMRFMQRVERPPLLAIVHQ 96 G G NVA+ +A LG +G LG DN + F +R + + + Sbjct: 39 GKGINVAQVLADLGHQLTVSGFLGEDNLQ----------AFEALFAKRGFVDAFIRVPGE 88 Query: 97 THPPAYFFMGENSADLAFDPAQLPAGW--------MGQVKWAHFGCI---SLVRQPIGNT 145 T + P + + + Q+ H + SL R Sbjct: 89 TRSNIKLAEADGRITDINGPGPVVSAAAQQALLDRLDQITLGHDAVVVAGSLPRGVSAQW 148 Query: 146 LATLAAELRSQGVKISFDPNYRNLMEHGYEPTLRKMAALADLIKVSDEDLRLIFKTDDEA 205 L L L+S+G+K++ D + L ++A LIK + E+L D EA Sbjct: 149 LHGLLLRLKSRGLKVALDTSGEALRAG--------LSAGPWLIKPNTEELSEAL--DCEA 198 Query: 206 GALAQLRAMNPAATVLVTRGPETAVLIDGA---------MVTEARPPRVEVVDTVGAGDA 256 ++A A AA+ L G E V+ GA A PPRV VV TVGAGD+ Sbjct: 199 ISVA---AQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHATPPRVSVVSTVGAGDS 255 Query: 257 SIGGLLFSLMTAPQRAWPEHLAFALAAGA 285 + G+L L++A A A+AA A Sbjct: 256 LLAGMLHGLLSADTPEQTLRTATAIAAMA 284 Lambda K H 0.321 0.134 0.412 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: 182 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 305 Length of database: 313 Length adjustment: 27 Effective length of query: 278 Effective length of database: 286 Effective search space: 79508 Effective search space used: 79508 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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