Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_013402452.1 CALHY_RS02545 sugar kinase
Query= BRENDA::Q42896 (328 letters) >NCBI__GCF_000166355.1:WP_013402452.1 Length = 316 Score = 184 bits (467), Expect = 2e-51 Identities = 115/310 (37%), Positives = 165/310 (53%), Gaps = 12/310 (3%) Query: 12 IVSFGEMLIDFVPTVSGVSLAEAPGFLKAPGGAPANVAIAVTRLGGKSAFVGKLGDDEFG 71 +V+ GE ++ F PT SG L F+K GGA AN AI + RLG K+ ++ KLG+DEFG Sbjct: 4 VVTIGEAMVVFNPTASG-PLRYVNNFVKKVGGAEANFAIGIVRLGHKAGWISKLGNDEFG 62 Query: 72 HMLAGILKTNGVQAEGINFDKGARTALAFVTLRADGEREFMFYRNPSADMLLTPAELNLD 131 + +++ GV + FD A T + F +R GE + +YR SA LTP +L+ D Sbjct: 63 KCILSVIRGEGVDTSQVKFDPEAPTGIYFKEIREYGETKVYYYRRGSAASRLTPEDLDPD 122 Query: 132 LIRSAKVFHYGSIS-LIVEPCRAAHMKAMEVAKEAGALLSYDPNLRLPLWPSAEEAKKQI 190 I SAK H I+ + E C +A+++AK G +S DPN+RL LW S E+A++ I Sbjct: 123 YIGSAKYLHVTGITPALSESCYLTIKEAIKIAKSRGVKISLDPNIRLKLW-SKEQARRVI 181 Query: 191 KSIWDSADVIKVSDVELEFLTGSNKIDDESAMSLWHPNLKLLLVTLGEKGCNYYTKKFHG 250 + + AD++ E E L G K + A + +++V LGEKG Y TK G Sbjct: 182 MELAEQADIVLPGITEGEILVG-EKNPENIAKKFLDLGVSIVVVKLGEKGAYYATKDESG 240 Query: 251 TVGGFHV-KTVDTTGAGDSFVGALLTKIVDDQTILEDEARLKEVLRFSCACGAITTTKKG 309 V GF + K VD GAGD F + ++ + + LKE ++ + A GAI TT G Sbjct: 241 YVSGFPIEKVVDPIGAGDGFAAGFIAGLLKNYS-------LKEAVKLANAVGAIATTVIG 293 Query: 310 AIPALPTASE 319 LPT E Sbjct: 294 DFEGLPTMEE 303 Lambda K H 0.318 0.135 0.389 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: 261 Number of extensions: 14 Number of successful extensions: 7 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: 328 Length of database: 316 Length adjustment: 28 Effective length of query: 300 Effective length of database: 288 Effective search space: 86400 Effective search space used: 86400 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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