Align galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate WP_015738480.1 ADEG_RS02275 galactose-1-phosphate uridylyltransferase
Query= metacyc::MONOMER-15710 (344 letters) >NCBI__GCF_000024605.1:WP_015738480.1 Length = 341 Score = 260 bits (665), Expect = 3e-74 Identities = 136/343 (39%), Positives = 199/343 (58%), Gaps = 22/343 (6%) Query: 10 PELRKDSVTNRWVIFSPARAKRPSDFKSKSPAPSSTDSPQTCPFCIGQEHHCAPEI--FR 67 PE RKD V +RWV S RAKRP+D++ P + CP C+G E PE+ FR Sbjct: 2 PEWRKDPVVDRWVAVSTERAKRPTDYRP----PLERKKQERCPLCVGHEGDTPPEVMAFR 57 Query: 68 FP---PQNPDWKVRVIQNLYPALSRDKDLDSSTSLSSGSLLWGCLLDGYGFHDVIIESPV 124 P P +P W VRV+ N +PA +++ G W C G G H+VI+E+P Sbjct: 58 HPGSLPDHPGWWVRVVPNKFPACRVEEE---DIVRPHGPYQWRC---GVGAHEVIVETPE 111 Query: 125 HSVHLSDLTPEDVAQVLFAYKKRILQLASDDSIKYVQVFKNHGASAGASMTHPHSQMVGL 184 H +L + + +A+V++A++ R+L L D KY+Q+FKN G+ AGAS+ H HSQ++ L Sbjct: 112 HVPNLVNQSEGQIAEVIWAWRARLLDLRRDTRFKYIQIFKNKGSVAGASLEHTHSQLIAL 171 Query: 185 PVIPPSVTTRLDSMKQYFNETGKCSICHVPTKDL-----LVDESVHFISVVPYAASFPFE 239 P++P + L +K Y E G C C + +L +V+ES HF+ VPYAA FPFE Sbjct: 172 PMVPAEIQAELTGVKVYREEKGSCVFCDLWRYELEAGERVVEESSHFLCFVPYAARFPFE 231 Query: 240 LWIVPRDHVSHFHELDQEKAVDLGGLLKVTLIKMSLQLNKPPFNFMIHTSPLQASDSDLA 299 +W+VP+ H F +++ + DL LLK TL +++ + PPFN ++HT+P+ + Sbjct: 232 MWLVPKRHKPDFGAIEEGEVCDLAWLLKRTLYRLAQTVFDPPFNLVLHTAPVNVPEP--V 289 Query: 300 YSHWFFQIVPHLSGVGGFELGTGCYINPVFPEDAAKVMREVNI 342 HW +I+P L+ + GFELGTG YINP PE AA +RE + Sbjct: 290 DYHWHIEILPRLTIMAGFELGTGYYINPTPPEMAAAALREQEV 332 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: 400 Number of extensions: 19 Number of successful extensions: 6 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: 341 Length adjustment: 29 Effective length of query: 315 Effective length of database: 312 Effective search space: 98280 Effective search space used: 98280 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