Align galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_089323653.1 CHB58_RS08345 DUF4931 domain-containing protein
Query= metacyc::MONOMER-15710 (344 letters) >NCBI__GCF_900188395.1:WP_089323653.1 Length = 328 Score = 176 bits (446), Expect = 7e-49 Identities = 110/339 (32%), Positives = 173/339 (51%), Gaps = 23/339 (6%) Query: 5 VESRRPELRKDSVTNRWVIFSPARAKRPSDFKSKSPAPSSTDSPQTCPFCIGQEHHCAPE 64 +E E+R + + +RW + S R KRP+DFK K A S++S CPF G EH E Sbjct: 1 MERLNREIRYNYLFDRWTLISADRGKRPTDFK-KLYAEKSSES-FICPFDAGNEHLTPRE 58 Query: 65 IFRFPPQNPDWKVRVIQNLYPALSRDKDLDSSTSLSSGSLLWGCLLDGYGFHDVIIESPV 124 N W VRV++N +PA+ LD+ L YG+H+V+IE+P Sbjct: 59 KLVLKKGNR-WIVRVVENKFPAVENGLLLDNGKGFFKR-------LPAYGYHEVVIETPE 110 Query: 125 HSVHLSDLTPEDVAQVLFAYKKRILQLASDDSIKYVQVFKNHGASAGASMTHPHSQMVGL 184 HS+ L D++ E++ +L A+K RI+ + D IK+VQ+FKN+ AG S++H HSQ+V Sbjct: 111 HSLQLQDMSVENIFYILKAWKNRIVYIKKDKKIKHVQIFKNYKKEAGCSLSHSHSQIVAT 170 Query: 185 PVIPPSVTTRLDSMKQYFNETGKCSICHVPTKDLLVDESVHF-----ISVVPYAASFPFE 239 I PSV L KQ+ N G C +C +++ +E + F ++ + +A F E Sbjct: 171 SFI-PSVQKTL--CKQFENYNG-CYLCDEIEQEISEEERMFFKTENVVAYLSFAPQFEGE 226 Query: 240 LWIVPRDHVSHFHELDQEKAVDLGGLLKVTLIKMSLQLNKPPFNFMIHTSPLQASDSDLA 299 + P H+ F E + V++ +K+ + + N PP+N + P Sbjct: 227 FIVAPLKHIHSFEETEDTFLVEVARSVKIAISALVSVFNNPPYNLALFIPPFNYD----G 282 Query: 300 YSHWFFQIVPHLSGVGGFELGTGCYINPVFPEDAAKVMR 338 HW ++ P +S GFE+ TG I+ +PE+ AK+ R Sbjct: 283 IFHWHIRVFPRISFHAGFEISTGTLISSRYPEEIAKLFR 321 Lambda K H 0.320 0.135 0.421 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: 283 Number of extensions: 20 Number of successful extensions: 5 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: 344 Length of database: 328 Length adjustment: 28 Effective length of query: 316 Effective length of database: 300 Effective search space: 94800 Effective search space used: 94800 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: 49 (23.5 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