GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Burkholderia phytofirmans PsJN

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate BPHYT_RS16735 BPHYT_RS16735 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__BFirm:BPHYT_RS16735
          Length = 634

 Score =  764 bits (1973), Expect = 0.0
 Identities = 379/601 (63%), Positives = 470/601 (78%), Gaps = 2/601 (0%)

Query: 2   HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61
           H ++L+VT+R+V RS+ TREAYLA I  A    P RG L CAN AHG AG    DK  ++
Sbjct: 5   HSQLLKVTQRVVERSKPTREAYLARIHQAQGKFPARGALSCANLAHGFAGLEGNDKLVIK 64

Query: 62  MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121
            +   N+ IVSSYN+MLSAH PY+++P+ IK+A RE G V QFAGG PAMCDGVTQG AG
Sbjct: 65  QIREPNIGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGVTQGNAG 124

Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181
           MELSL SREVIA+STAVAL+HNMFDAAL LGICDKIVPGL++GAL+FGH+PTIFVP GPM
Sbjct: 125 MELSLFSREVIAMSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHIPTIFVPAGPM 184

Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            SG+SN +KA  RQ +A G+  R  LLE+E  +YHS GTCTFYGTAN+NQ+LMEVMGLHL
Sbjct: 185 GSGLSNDDKAKTRQLFATGQCDRGALLEAEAAAYHSHGTCTFYGTANSNQMLMEVMGLHL 244

Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301
           P ++FV+P+TPLRDALT +AA++V  LT + GN+TPIG +VDE+++VN IVAL ATGGST
Sbjct: 245 PSSAFVHPHTPLRDALTAQAARRVLELTVERGNYTPIGHVVDEKAIVNGIVALLATGGST 304

Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361
           NHTLH+ AIA+AAGI + W D   LS+ VP L+ +YPNGKAD+NHF AAGG+AFL+R LL
Sbjct: 305 NHTLHLVAIARAAGIVIDWDDFDTLSQAVPLLAKIYPNGKADVNHFHAAGGVAFLVRNLL 364

Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLR 421
           E GLLHEDVNTVAG+GL  YT+EP L +GKL W  G   S D  +LR +   F P+GGLR
Sbjct: 365 EGGLLHEDVNTVAGKGLKHYTEEPKLIDGKLQWVPGAQASEDTAVLRGIKEPFQPDGGLR 424

Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481
           +M+G LGRGV+K+SAVA QH+ V+APA+VF  Q+ + +AF  GEL++DF+AV+RFQG R+
Sbjct: 425 LMQGKLGRGVIKISAVAAQHRKVKAPAIVFDSQEAVQEAFDKGELKRDFIAVVRFQGARA 484

Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541
           NGMPELH++TP LGVLQD+GF VALVTDGRMSGASGK+PA IH+SPEA + G + +VR G
Sbjct: 485 NGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRTG 544

Query: 542 DIIRVDGVKGTLELKVDADEFAAREPA--KGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599
           D++ +D   G L++++DA E+AAR  A  +    N VG GRELF   R A + AEQGAS 
Sbjct: 545 DMLVIDAEAGVLDIEIDAAEWAARPNAVPQHQAENEVGFGRELFSVFRAAAAPAEQGASV 604

Query: 600 F 600
           F
Sbjct: 605 F 605


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: 1168
Number of extensions: 43
Number of successful extensions: 2
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: 634
Length adjustment: 37
Effective length of query: 571
Effective length of database: 597
Effective search space:   340887
Effective search space used:   340887
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 BPHYT_RS16735 BPHYT_RS16735 (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.7138.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.9e-300  982.6   1.1   3.4e-300  982.5   1.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16735  BPHYT_RS16735 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16735  BPHYT_RS16735 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  982.5   1.1  3.4e-300  3.4e-300       1     600 [.       5     605 ..       5     606 .. 0.99

  Alignments for each domain:
  == domain 1  score: 982.5 bits;  conditional E-value: 3.4e-300
                                TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaii 70 
                                              hs+l+++t+r++ersk+tre+yl++i++a+ k + r++l+c+nlahg+a l+ ++k+ +k+ +++n++i+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735   5 HSQLLKVTQRVVERSKPTREAYLARIHQAQGKFPARGALSCANLAHGFAGLEGNDKLVIKQIREPNIGIV 74 
                                              89******************************************************************** PP

                                TIGR01196  71 tayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaigls 140
                                              ++yn+mlsah p+k+ypd+ik+a++e+++vaq agGvpamcdGvtqG++Gmelsl+sr+via+sta++l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735  75 SSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGVTQGNAGMELSLFSREVIAMSTAVALT 144
                                              ********************************************************************** PP

                                TIGR01196 141 hnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellkse 210
                                              hnmfd+al+lG+cdkivpGlli+al fGh+p++fvpaGpm sGl+n++kak+rqlfa G+ dr +ll++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 145 HNMFDAALCLGICDKIVPGLLIGALQFGHIPTIFVPAGPMGSGLSNDDKAKTRQLFATGQCDRGALLEAE 214
                                              ********************************************************************** PP

                                TIGR01196 211 masyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplael 280
                                              +a+yh+ GtctfyGtansnqml+e+mGlhlp+++fv+p+tplrdalt++aa+r+ +lt + g+++p++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 215 AAAYHSHGTCTFYGTANSNQMLMEVMGLHLPSSAFVHPHTPLRDALTAQAARRVLELTVERGNYTPIGHV 284
                                              ********************************************************************** PP

                                TIGR01196 281 ideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaG 350
                                              +dek+ivn++v+llatGGstnhtlhlvaiaraaGi+++wdd++ ls+ vplla++ypnGkadvnhf+aaG
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 285 VDEKAIVNGIVALLATGGSTNHTLHLVAIARAAGIVIDWDDFDTLSQAVPLLAKIYPNGKADVNHFHAAG 354
                                              ********************************************************************** PP

                                TIGR01196 351 GlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlk 420
                                              G++fl+r+ll+ Gllhedv+tvagkGl++yt+ep+l dgkl++ ++a++s d+++lr +++pf+++GGl+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 355 GVAFLVRNLLEGGLLHEDVNTVAGKGLKHYTEEPKLIDGKLQWVPGAQASEDTAVLRGIKEPFQPDGGLR 424
                                              ********************************************************************** PP

                                TIGR01196 421 llkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklt 490
                                              l++G lGr+vik+sav+ ++r+++apaivf++q+ +++af++gel+rd++avvrfqG +anGmpelh+lt
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 425 LMQGKLGRGVIKISAVAAQHRKVKAPAIVFDSQEAVQEAFDKGELKRDFIAVVRFQGARANGMPELHRLT 494
                                              ********************************************************************** PP

                                TIGR01196 491 tvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddae 560
                                              + lGvlqd+gf valvtdGr+sGasGkvpa ih++peal +G++ k+r+Gd++ +da +g l++ +d ae
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 495 PLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRTGDMLVIDAEAGVLDIEIDAAE 564
                                              ********************************************************************** PP

                                TIGR01196 561 lkareleeld.lednelGlGrelfaalrekvssaeeGassl 600
                                              ++ar  + ++   +ne+G Grelf+ +r +++ ae+Gas++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16735 565 WAARPNAVPQhQAENEVGFGRELFSVFRAAAAPAEQGASVF 605
                                              *****99998466799**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (634 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.96
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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