Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_110805670.1 C8J30_RS09805 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_003217355.1:WP_110805670.1 Length = 606 Score = 692 bits (1785), Expect = 0.0 Identities = 357/599 (59%), Positives = 430/599 (71%), Gaps = 4/599 (0%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 ++ + VT+R+ ARS A R YLA I A + GP R L C N AH A G DK L Sbjct: 8 LNATIARVTDRIRARSAARRGDYLARIAAAMAQGPARAHLACGNQAHAYAAMGP-DKAPL 66 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 N+ IV++YNDMLSAH PY +P QIK ALR +G+ Q AGG PAMCDGVTQG A Sbjct: 67 AEGRGPNIGIVTAYNDMLSAHAPYADYPAQIKAALRAIGATAQVAGGVPAMCDGVTQGRA 126 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSL SR+VIAL+ VALSH+ FDAA+ LG+CDKIVPGL+M A FGHLP IF+P GP Sbjct: 127 GMELSLFSRDVIALAAGVALSHDTFDAAIFLGVCDKIVPGLVMAAATFGHLPAIFLPAGP 186 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 M +G+ N EKA VRQ++A G+ R++L+ +EM SYH PGTCTFYGTANTNQ+LMEVMGLH Sbjct: 187 MTAGLPNDEKAKVRQQFATGEVGRDKLMAAEMASYHGPGTCTFYGTANTNQMLMEVMGLH 246 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPGASFVNP+TPLRDALT A +V +T N P+G ++DER+ VN +V L ATGGS Sbjct: 247 LPGASFVNPHTPLRDALTVAGAHRVAAITALGENALPVGHLLDERAFVNGLVGLMATGGS 306 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TN LH+PA+A+AAGI+L +D D+S VP ++ VYPNG AD+N F AAGG+ FLIR L Sbjct: 307 TNLVLHLPAMARAAGIELDLEDFDDISATVPLMAKVYPNGLADVNAFHAAGGLQFLIRHL 366 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 L AGLLH DVNTVAG GL+RYTQ+ L G+L W +GP +SL++ ILRP A F+ GGL Sbjct: 367 LRAGLLHADVNTVAGPGLARYTQDAKLIEGRLTWVEGPEDSLNDRILRPAATPFAATGGL 426 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 + + GNLGRGV+KVSAVA ++EAPA VF+ Q + DAFK GE +D V V+RFQGP+ Sbjct: 427 KHLAGNLGRGVIKVSAVAPDRHVIEAPARVFESQDAVKDAFKRGEFTRDTVVVVRFQGPQ 486 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 +NGMPELH +TP L VLQDRG +VALVTDGRMSGASGK+PAAIHVSPEA GG LAR+ D Sbjct: 487 ANGMPELHSLTPTLSVLQDRGLRVALVTDGRMSGASGKVPAAIHVSPEAACGGPLARLLD 546 Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPA-KGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598 GD+IR+D GTL + F R PA L N G GRELF R A GAS Sbjct: 547 GDLIRLDADTGTLTCLTEG--FETRAPATPDLSANRTGLGRELFETFRRNTGPATSGAS 603 Lambda K H 0.318 0.134 0.386 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: 1083 Number of extensions: 48 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: 608 Length of database: 606 Length adjustment: 37 Effective length of query: 571 Effective length of database: 569 Effective search space: 324899 Effective search space used: 324899 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_110805670.1 C8J30_RS09805 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))
# 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/TIGR01196.hmm # target sequence database: /tmp/gapView.1961490.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01196 [M=601] Accession: TIGR01196 Description: edd: phosphogluconate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-287 940.8 0.9 1.6e-287 940.6 0.9 1.0 1 NCBI__GCF_003217355.1:WP_110805670.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217355.1:WP_110805670.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 940.6 0.9 1.6e-287 1.6e-287 2 600 .. 10 605 .. 9 606 .] 0.99 Alignments for each domain: == domain 1 score: 940.6 bits; conditional E-value: 1.6e-287 TIGR01196 2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 + +a++t+ri +rs++ r yl++i +a +g+ r++l+cgn ah++aa+ + +k++l++ + +n++i+tayn NCBI__GCF_003217355.1:WP_110805670.1 10 ATIARVTDRIRARSAARRGDYLARIAAAMAQGPARAHLACGNQAHAYAAMGP-DKAPLAEGRGPNIGIVTAYN 81 5799**********************************************98.69****************** PP TIGR01196 75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147 dmlsah p+++yp++ik al+ +a+aqvagGvpamcdGvtqG++Gmelsl+srdvial+++++lsh+ fd+a NCBI__GCF_003217355.1:WP_110805670.1 82 DMLSAHAPYADYPAQIKAALRAIGATAQVAGGVPAMCDGVTQGRAGMELSLFSRDVIALAAGVALSHDTFDAA 154 ************************************************************************* PP TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220 +flGvcdkivpGl++aa++fGhlpa+f+paGpm++Gl+n+ekakvrq+fa G v+r++l+++emasyh+pGtc NCBI__GCF_003217355.1:WP_110805670.1 155 IFLGVCDKIVPGLVMAAATFGHLPAIFLPAGPMTAGLPNDEKAKVRQQFATGEVGRDKLMAAEMASYHGPGTC 227 ************************************************************************* PP TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293 tfyGtan+nqml+e+mGlhlpgasfvnp+tplrdalt + a+r+a++ta +++ lp+++l+de+++vn+lvgl NCBI__GCF_003217355.1:WP_110805670.1 228 TFYGTANTNQMLMEVMGLHLPGASFVNPHTPLRDALTVAGAHRVAAITALGENALPVGHLLDERAFVNGLVGL 300 ************************************************************************* PP TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366 +atGGstn lhl a+araaGi l+ +d++++s vpl+a+vypnG advn+f+aaGGl+flir+ll++Gllh NCBI__GCF_003217355.1:WP_110805670.1 301 MATGGSTNLVLHLPAMARAAGIELDLEDFDDISATVPLMAKVYPNGLADVNAFHAAGGLQFLIRHLLRAGLLH 373 ************************************************************************* PP TIGR01196 367 edvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439 dv+tvag Gl ryt++++l +g+l++ e++e sl++ ilr++ +pf+a+GGlk l GnlGr+vikvsav+++ NCBI__GCF_003217355.1:WP_110805670.1 374 ADVNTVAGPGLARYTQDAKLIEGRLTWVEGPEDSLNDRILRPAATPFAATGGLKHLAGNLGRGVIKVSAVAPD 446 ************************************************************************* PP TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512 +vieapa+vf++q +++afk+ge+ rd v+vvrfqGp+anGmpelh lt++l vlqdrg +valvtdGr+s NCBI__GCF_003217355.1:WP_110805670.1 447 RHVIEAPARVFESQDAVKDAFKRGEFTRDTVVVVRFQGPQANGMPELHSLTPTLSVLQDRGLRVALVTDGRMS 519 ************************************************************************* PP TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585 GasGkvpaaihv+pea+ gG+la++ dGdlirlda +g l+ l + +e +r ++++dl++n+ GlGrelf + NCBI__GCF_003217355.1:WP_110805670.1 520 GASGKVPAAIHVSPEAACGGPLARLLDGDLIRLDADTGTLTCLTEGFE--TRAPATPDLSANRTGLGRELFET 590 ********************************************9987..67788****************** PP TIGR01196 586 lrekvssaeeGassl 600 +r++++ a +Gas++ NCBI__GCF_003217355.1:WP_110805670.1 591 FRRNTGPATSGASVI 605 ************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (606 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 27.74 // [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