Alignments for a candidate for edd in Burkholderia phytofirmans PsJN

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.29800.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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.51
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources