Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate WP_011842355.1 RSPH17029_RS17265 ribokinase
Query= curated2:P23386 (316 letters) >NCBI__GCF_000015985.1:WP_011842355.1 Length = 292 Score = 56.2 bits (134), Expect = 9e-13 Identities = 90/304 (29%), Positives = 116/304 (38%), Gaps = 29/304 (9%) Query: 11 NSAVDQTVTVPGFTADAVNRV-AASRIDAGGKGVNVASFLAHVGHGVAVTGLLG-AENAA 68 N A+D+T+++ F + AA D GGKG N A + G +G Sbjct: 8 NVALDETLSIEDFPRPGASIFGAALSRDLGGKGANQAVAMGRTGLACIFVSAVGQGPRGQ 67 Query: 69 LFARHFAATGLVDACQRLPGATRTNVKIVDPLQDQVTDLNFPGIAAGPADLDAVAATLTE 128 A+ A L L G T++ IV + AA +A AA L Sbjct: 68 EIAQRLAQEPLEAELVALEGVA-TDISIVLMSARGENAIITTREAASALTPEAAAAALAR 126 Query: 129 LLAQGLDWVALCGSLPAGIGAEAYAELAALARKGGARVALDTSG--PALGLALAARPDIV 186 Q D + L G+L A A A L A AR G R A + S P G L D V Sbjct: 127 --GQTGDLLVLQGNLSA---AATQAALRA-ARDAGMRTAFNPSPLQPYFG-TLWPLVDTV 179 Query: 187 KPNVAELGAHLGRTLTGLESVREAARDLAASGVGLVAVSMGAGGAVLVRGAEAVLAIPPA 246 N E A L G+ES L A GVG + +++GA GA L+R E Sbjct: 180 FLNEGEAEA-----LGGVES-------LLAQGVGEIVLTLGAQGAELIRATERTRVPAHP 227 Query: 247 TPIASTVGAGDA-MVAGLIHAATLGLDL----AETARLATAFSLGALGEIGPHLPPPERL 301 + T GAGD M L AA G L A A A ++G G + E Sbjct: 228 CAVVDTTGAGDCFMAVALASAALRGTRLDARALNHAARAAAHTVGRAGTVAAFPNRAEMA 287 Query: 302 AALA 305 A LA Sbjct: 288 AILA 291 Lambda K H 0.318 0.133 0.377 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: 207 Number of extensions: 11 Number of successful extensions: 2 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: 316 Length of database: 292 Length adjustment: 27 Effective length of query: 289 Effective length of database: 265 Effective search space: 76585 Effective search space used: 76585 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 Apr 10 2024. 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