Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate WP_072908932.1 BUB13_RS11620 mannose-1-phosphate guanyltransferase
Query= BRENDA::P74285 (388 letters) >NCBI__GCF_900142125.1:WP_072908932.1 Length = 838 Score = 187 bits (475), Expect = 1e-51 Identities = 105/323 (32%), Positives = 177/323 (54%), Gaps = 16/323 (4%) Query: 1 MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60 MKA+I+A G GTR+ P++ +PKPM+P+ +P+M +++LL++HG ++++ + + + Sbjct: 1 MKAVIMAGGFGTRLHPLSINLPKPMVPLCNRPIMLHIVDLLKKHGITELVMLLYFQPDTV 60 Query: 61 ESYFRDGQRFGVQIAYSFEGNIVDGDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDAL 120 + +F DG +GV I Y + LG+AG +K D+ F+++ GD L Sbjct: 61 KKFFGDGSEYGVNITYVTPL---------EDLGTAGAVKAAARH---LDERFLIISGDLL 108 Query: 121 IDLDLTTAVKLHREKGAIATIITKTVPQELVSSYGVVVTDDNGKILTFQEKPAVEEALST 180 D DLT A+K H K A AT+ +VP L +GVV+T+ G+I F EKP E S Sbjct: 109 TDFDLTAAIKFHEAKNAKATLTLTSVPDPL--QFGVVITNQKGEITKFLEKPDWGEVFSD 166 Query: 181 EINTGIYIFEPEVIDYIPSGQEYDLGGDLFPKLVDSGLPFYAVNMDFEWVDIGKVPDYWQ 240 INTGIYI EPEV+D IP G+ D D+FP+L+ Y + W DIG Y + Sbjct: 167 TINTGIYILEPEVLDLIPEGENRDWSKDIFPQLLQQKDRLYGCTLKGYWQDIGNTDAYLE 226 Query: 241 AIRGVLSREIKNVQIPGIEVRPGVYTGINVAANWDNIE-IEGPVYIGGMTRIEDGVKIIG 299 + +++ +++ + + V+ G + + D + + G V +G TR+ K+ Sbjct: 227 TCKDIMAGKVEIEIDETLTEKKKVFFGAETSVSEDTQKALRGMVVLGDNTRLVGKPKLKN 286 Query: 300 PSMIGPSCLICQGAVVDNSVIFE 322 +IG +C I GA +++ ++++ Sbjct: 287 -CLIGRNCTIEDGAELEDCILWD 308 Lambda K H 0.321 0.141 0.418 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: 717 Number of extensions: 28 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: 388 Length of database: 838 Length adjustment: 36 Effective length of query: 352 Effective length of database: 802 Effective search space: 282304 Effective search space used: 282304 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 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