Align UTP--glucose-1-phosphate uridylyltransferase; Alpha-D-glucosyl-1-phosphate uridylyltransferase; General stress protein 33; GSP33; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase; EC 2.7.7.9 (characterized)
to candidate CCNA_03752 CCNA_03752 UTP-glucose-1-phosphate uridylyltransferase
Query= SwissProt::Q05852 (292 letters) >FitnessBrowser__Caulo:CCNA_03752 Length = 298 Score = 286 bits (731), Expect = 5e-82 Identities = 145/277 (52%), Positives = 192/277 (69%), Gaps = 2/277 (0%) Query: 1 MKKVRKAIIPAAGLGTRFLPATKAMPKEMLPIVDKPTIQYIIEEAVEAGIEDIIIVTGKS 60 MK VRKA++P AGLGTR LP TK PKE+L +VD+P + YI+EE +AGIE + VTG+S Sbjct: 8 MKPVRKAVLPVAGLGTRVLPGTKTTPKELLNVVDRPILSYIVEEGRKAGIEHFVFVTGRS 67 Query: 61 KRAIEDHFDYSPELERNLEEKGKTELLEKVK-KASNLADIHYIRQKEPKGLGHAVWCARN 119 K AIED+FD+ ELE LE KGK E+LE+++ + ++ ++RQ P GLGHAVWCAR+ Sbjct: 68 KGAIEDYFDHQIELEAQLEAKGKIEILEQLRAELPKPGEMSFVRQMAPLGLGHAVWCARD 127 Query: 120 FIGDEPFAVLLGDDIVQAETPGLRQLMDEYEKTLS-SIIGVQQVPEEETHRYGIIDPLTS 178 IGDEPFAV+L D IV AE L QL+D Y K ++IGV++VPE ETH+YG++ P Sbjct: 128 IIGDEPFAVMLPDVIVDAERACLGQLIDLYNKVGGGNVIGVEEVPESETHKYGVVAPGKV 187 Query: 179 EGRRYQVKNFVEKPPKGTAPSNLAILGRYVFTPEIFMYLEEQQVGAGGEIQLTDAIQKLN 238 +GR + VEKP KGTAPSN AI GRY+ PEIF L Q+ GAG EIQLTD++ KL Sbjct: 188 DGRMATMTGMVEKPAKGTAPSNWAIAGRYILQPEIFALLAAQEKGAGNEIQLTDSMAKLM 247 Query: 239 EIQRVFAYDFEGKRYDVGEKLGFITTTLEFAMQDKEL 275 + Q AY +EG +D G+K+G + + A++ +L Sbjct: 248 QDQAFHAYVYEGVTHDCGDKIGLLRANVALALKRADL 284 Lambda K H 0.317 0.138 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: 254 Number of extensions: 7 Number of successful extensions: 3 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: 292 Length of database: 298 Length adjustment: 26 Effective length of query: 266 Effective length of database: 272 Effective search space: 72352 Effective search space used: 72352 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 (21.6 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