Align galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate NP_349448.1 CA_C2844 galactose-1-phosphate uridylyltransferase
Query= metacyc::MONOMER-15710 (344 letters) >NCBI__GCF_000008765.1:NP_349448.1 Length = 314 Score = 185 bits (469), Expect = 2e-51 Identities = 102/336 (30%), Positives = 181/336 (53%), Gaps = 29/336 (8%) Query: 12 LRKDSVTNRWVIFSPARAKRPSDFKSKSPAPSSTDSPQTCPFCIGQEHHCAPEIFRFPPQ 71 +R++S+ N VI + RA+RP + KSK + CPFCIG E+ I+ Sbjct: 3 IRRNSINNTTVIINKKRAERPVELKSKKKKEEKVQYEKECPFCIGNEYRTPAVIY---DT 59 Query: 72 NPDWKVRVIQNLYPALSRDKDLDSSTSLSSGSLLWGCLLDGYGFHDVIIESPVHSVHLSD 131 + VRV +N YP + ++K +D++ + +G H V+IE HS ++ + Sbjct: 60 KEPYHVRVSENKYPIV-KEKSMDNN--------------EVFGNHYVVIEGKNHSDNMYE 104 Query: 132 LTPEDVAQVLFAYKKRILQLASDDSIKYVQVFKNHGASAGASMTHPHSQMVGLPVIPPSV 191 T E + +++ AYK + +L ++ IKYVQ+FKN G +GAS+ HPHSQ+VG+ ++P + Sbjct: 105 FTKEQMREIIKAYKNTVYKLYENEDIKYVQIFKNCGKDSGASLKHPHSQIVGINIVPDEI 164 Query: 192 TTRLDSMKQYFNETGKCSIC-----HVPTKDLLVDESVHFISVVPYAASFPFELWIVPRD 246 + + K+Y+ E +C C V K ++ +F + PY +++ +++ I+ Sbjct: 165 SREIKGTKKYYEENKECFYCSRLKKEVQYKKRIIHMGKYFTAFCPYDSTYQYKVTIMKNK 224 Query: 247 HVSHFHELDQEKAVDLGGLLKVTLIKMSLQLNKPPFNFMIHTSPLQASDSDLAYSHWFFQ 306 H S+F LD+ + ++LG ++ + L K++ +N H + + H++ Sbjct: 225 HQSNF-GLDELEMMELGEIITLILKKLNNISYNCSYNMCFH-----FLKEENEFYHFYVD 278 Query: 307 IVPHLSGVGGFELGTGCYINPVFPEDAAKVMREVNI 342 I+P L+ +GGFE+GTG IN V PE AA++ R + + Sbjct: 279 IIPRLNPMGGFEIGTGIMINTVDPEVAAEIFRNIQL 314 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: 243 Number of extensions: 17 Number of successful extensions: 4 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: 314 Length adjustment: 28 Effective length of query: 316 Effective length of database: 286 Effective search space: 90376 Effective search space used: 90376 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