Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_003465239.1 J416_RS03825 UDP-glucose--hexose-1-phosphate uridylyltransferase
Query= curated2:Q9KDV2 (508 letters) >NCBI__GCF_000359605.1:WP_003465239.1 Length = 499 Score = 516 bits (1329), Expect = e-151 Identities = 263/507 (51%), Positives = 352/507 (69%), Gaps = 12/507 (2%) Query: 4 SSIAIQIEALLTYALQHGLITKWDIDASRNRVLDVLDLDE-LEPVEQVDVECEMPYPILE 62 ++++ +E L+ A+ +IT+ D +RN++L L ++E +E V ++P +LE Sbjct: 2 TNLSQTVEVLVQRAIDKSMITRQDAIYARNQILSYLHVNEFIEEQSLAHVNDDIP-DLLE 60 Query: 63 NILDWAAENGRLEANTVTYRDLLDTKLMGALLGQPSETIRTFYERYEQQGPEEATKVFYD 122 ++ D+AA + +E + + R+ L ++M + +PSE RTFY++YE+ P AT FY Sbjct: 61 SLTDYAARHNIIE-DLLDEREKLSAQMMNVFVSKPSEINRTFYQKYEES-PVLATDFFYQ 118 Query: 123 FSKQVHYIRTDRIAKNEHWFSETPYGQLEITINLSKPEKDPKAIAQAKHL-QASSYPKCL 181 FSK +YI+T RIAKN + + + YG L+ITINLSKPEKDP+ I + + L Q +YP+CL Sbjct: 119 FSKDTNYIQTKRIAKNIEFVTPSAYGDLDITINLSKPEKDPEQIKRERELKQEIAYPQCL 178 Query: 182 LCKENVGYRGRVNHPARQNLRVIPVELNQEQWYMQFSPYVYYNEHAIVFSGEHVPMKIST 241 LCKEN GY GR+ HPAR N R+I + L E W+ Q+SPYVYYNEH+IVFS EH PM I+ Sbjct: 179 LCKENEGYAGRIGHPARSNHRIIEIPLEGETWFFQYSPYVYYNEHSIVFSSEHRPMTITR 238 Query: 242 ETFARLLEFTEKFPHYFIGSNADLPIVGGSILSHDHFQGGNHAFPMAKASMEKTFSISRF 301 +TF+RL F E+FPHYFIGSNADLPIVGGSILSHDH+Q G + F M A E FSI F Sbjct: 239 DTFSRLTAFVEQFPHYFIGSNADLPIVGGSILSHDHYQAGRYTFAMTNAEDEFRFSIDPF 298 Query: 302 PSVIAGIVKWPMSVVRLQGMDRSELVKAADHVYHAWQAYGDEAADIYPFTGDTPHNTITP 361 PS+ A +VKWP+SV+RL+ DR LV AA H+ W+ Y D A+I +T TPHNTITP Sbjct: 299 PSIEASVVKWPLSVIRLRHEDRHYLVNAAHHILTKWRDYSDPDANIVAYTEKTPHNTITP 358 Query: 362 IARRRGELFELDLVLRNNRTSKEHPDGIFHPHQEVHHIKKENIGLIEVMGLAVLPGRLKE 421 IAR+RG FELDLVLRNNRT+K+HP G+FHPH++VHHIKKENIGLIEVMGLAVLP RLK+ Sbjct: 359 IARKRGNQFELDLVLRNNRTTKQHPAGLFHPHEDVHHIKKENIGLIEVMGLAVLPPRLKD 418 Query: 422 ELELLAEALLSSDPRQVIARYEQIQKHEAWALAIKERHAHLHDSNVMDILRDEIGKVFAT 481 ELE + +ALL + +A Y H+ W +IK+RH+ + + V I+ E+G+ FA Sbjct: 419 ELETIKQALLGEN--VTVADY-----HQNWVQSIKKRHSLITEETVTQIVEQELGEKFAR 471 Query: 482 ILAHAGVFKRTGEGAAAFDRFISTLNQ 508 +L AGV+KR G AF RFI T+N+ Sbjct: 472 VLEDAGVYKRDRAGRQAFQRFIDTVNE 498 Lambda K H 0.319 0.135 0.404 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: 683 Number of extensions: 32 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: 508 Length of database: 499 Length adjustment: 34 Effective length of query: 474 Effective length of database: 465 Effective search space: 220410 Effective search space used: 220410 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: 52 (24.6 bits)
Align candidate WP_003465239.1 J416_RS03825 (UDP-glucose--hexose-1-phosphate uridylyltransferase)
to HMM TIGR01239 (galT: galactose-1-phosphate uridylyltransferase (EC 2.7.7.12))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01239.hmm # target sequence database: /tmp/gapView.69168.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01239 [M=489] Accession: TIGR01239 Description: galT_2: galactose-1-phosphate uridylyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-209 682.6 5.1 2.3e-209 682.4 5.1 1.0 1 NCBI__GCF_000359605.1:WP_003465239.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359605.1:WP_003465239.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 682.4 5.1 2.3e-209 2.3e-209 2 489 .] 8 496 .. 7 496 .. 0.98 Alignments for each domain: == domain 1 score: 682.4 bits; conditional E-value: 2.3e-209 TIGR01239 2 veefieqalenkdieeldrlylrnkllellglesadeekkesekvnqssldlldqllkaaaenglleevkeqk 74 ve +++ a++++ i ++d +y rn++l l +++ ee++ +vn+ +dll+ l + aa+ + +e++ +++ NCBI__GCF_000359605.1:WP_003465239.1 8 VEVLVQRAIDKSMITRQDAIYARNQILSYLHVNEFIEEQSL-AHVNDDIPDLLESLTDYAARHNIIEDLLDER 79 7889*****************************99777665.567789************************* PP TIGR01239 75 elleaklldlitPrPskvnrefwekykssPeqatkefyqlskrveyvktdaiakniaykaetkyGdleitinl 147 e l+a+++++++ +Ps++nr f++ky+ sP at+ fyq+sk+++y++t++iakni++ +++ yGdl+itinl NCBI__GCF_000359605.1:WP_003465239.1 80 EKLSAQMMNVFVSKPSEINRTFYQKYEESPVLATDFFYQFSKDTNYIQTKRIAKNIEFVTPSAYGDLDITINL 152 ************************************************************************* PP TIGR01239 148 skPekdpkaiaaakeakas.syPacqlcleneGflGsvnkparsnhrivrvsledeewgfqfsPyayfnehsi 219 skPekdp +i + +e k+ yP+c+lc+eneG+ G++ +parsnhri+++ le+e w+fq+sPy+y+nehsi NCBI__GCF_000359605.1:WP_003465239.1 153 SKPEKDPEQIKRERELKQEiAYPQCLLCKENEGYAGRIGHPARSNHRIIEIPLEGETWFFQYSPYVYYNEHSI 225 **************9987549**************************************************** PP TIGR01239 220 vlkekhePmeiskktferllsflekfPhyfiGsnadlPivGGsilshdhyqgGrhdfPmekaelkekveledy 292 v++++h+Pm i + tf+rl +f+e+fPhyfiGsnadlPivGGsilshdhyq+Gr++f m +ae + +++++ + NCBI__GCF_000359605.1:WP_003465239.1 226 VFSSEHRPMTITRDTFSRLTAFVEQFPHYFIGSNADLPIVGGSILSHDHYQAGRYTFAMTNAEDEFRFSIDPF 298 ************************************************************************* PP TIGR01239 293 pdvsagivkwPmsvlrlksedkgelaeaadkilktwksysdekldikaksdgtphhtvtPiarrrddkyeldl 365 p ++a++vkwP+sv+rl+ ed++ l++aa +il +w+ ysd ++i a+++ tph+t+tPiar+r++++eldl NCBI__GCF_000359605.1:WP_003465239.1 299 PSIEASVVKWPLSVIRLRHEDRHYLVNAAHHILTKWRDYSDPDANIVAYTEKTPHNTITPIARKRGNQFELDL 371 ************************************************************************* PP TIGR01239 366 vlrdnqtseeyPdGifhPhkdvhhikkeniGlievmGlailPgrlkkelkevekyllgqdnqlaeihkewadk 438 vlr+n+t +++P G+fhPh+dvhhikkeniGlievmGla+lP+rlk+el ++++llg++ ++a+ h++w + NCBI__GCF_000359605.1:WP_003465239.1 372 VLRNNRTTKQHPAGLFHPHEDVHHIKKENIGLIEVMGLAVLPPRLKDELETIKQALLGENVTVADYHQNWVQS 444 ************************************************************************* PP TIGR01239 439 lkeke.nitkenvkevvkeevgevfarvledaGvfkqtaeGkkafrkfidfl 489 +k+++ it+e+v+++v++e+ge farvledaGv+k G++af++fid++ NCBI__GCF_000359605.1:WP_003465239.1 445 IKKRHsLITEETVTQIVEQELGEKFARVLEDAGVYKRDRAGRQAFQRFIDTV 496 *9998679******************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (489 nodes) Target sequences: 1 (499 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 19.84 // [ok]
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