GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas fluorescens FW300-N2E2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Pf6N2E2_2898 Phosphogluconate dehydratase (EC 4.2.1.12)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898
          Length = 608

 Score = 1134 bits (2933), Expect = 0.0
 Identities = 571/607 (94%), Positives = 591/607 (97%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERL+ARSRATR+AYLALIRGAASDGP RGKLQCANFAHGVAGCG+EDKH L
Sbjct: 1   MHPRVLEVTERLIARSRATRQAYLALIRGAASDGPTRGKLQCANFAHGVAGCGTEDKHHL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMNAAN+AIVSSYNDMLSAHQPYE FPEQIKKALRE+GSVGQFAGGTPAMCDGVTQGEA
Sbjct: 61  RMMNAANIAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEA 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSLPSREVIALSTAVALSHNMFD ALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP
Sbjct: 121 GMELSLPSREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLRDALT EAA QVTR+TKQSGNF PIGEIVDERSLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLHMPAIA AAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL
Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHE+VNTV G GLSRYTQEPFL++G+LVWRDGPIESLDENILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHENVNTVLGHGLSRYTQEPFLEDGELVWRDGPIESLDENILRPVARAFSPEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVAL++Q+VEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVALENQVVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEA VGGALARV++
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQE 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDIIRVDGVKGTLELKVDA+EFAAR PAKGLLGNN+G+GRELFGFMRMAFSSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAARTPAKGLLGNNIGTGRELFGFMRMAFSSAEQGASAF 600

Query: 601 TSALENL 607
           TSALE L
Sbjct: 601 TSALETL 607


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: 1374
Number of extensions: 50
Number of successful extensions: 1
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: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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 Pf6N2E2_2898 (Phosphogluconate dehydratase (EC 4.2.1.12))
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.29031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
          0 1028.8   0.6          0 1028.6   0.6    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898  Phosphogluconate dehydratase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898  Phosphogluconate dehydratase (EC 4.2.1.12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1028.6   0.6         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1028.6 bits;  conditional E-value: 0
                                      TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekr 64 
                                                    h+r++e+ter+i+rs++tr++yl+ ir a++ g+ r++l c+n+ahgva +  ++k +l+ ++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898   2 HPRVLEVTERLIARSRATRQAYLALIRGAASDGPTRGKLQCANFAHGVAGCGTEDKHHLRMMNA 65 
                                                    79************************************************************** PP

                                      TIGR01196  65 knlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsr 128
                                                    +n+ai+++yndmlsahqp++++p++ikkal+e ++v+q agG+pamcdGvtqGe+Gmelsl sr
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898  66 ANIAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEAGMELSLPSR 129
                                                    **************************************************************** PP

                                      TIGR01196 129 dvialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakv 192
                                                    +vialsta++lshnmfdgal+lG+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nkeka v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 130 EVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKEKADV 193
                                                    **************************************************************** PP

                                      TIGR01196 193 rqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdal 256
                                                    rq +aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntplrdal
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 194 RQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDAL 257
                                                    **************************************************************** PP

                                      TIGR01196 257 treaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwd 320
                                                    treaa +++r+t ++g+++p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi+l+w+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 258 TREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGIQLTWQ 321
                                                    **************************************************************** PP

                                      TIGR01196 321 dlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkep 384
                                                    d+ +ls++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhe+v+tv+g+Gl+ryt+ep
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 322 DMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHENVNTVLGHGLSRYTQEP 385
                                                    **************************************************************** PP

                                      TIGR01196 385 fledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapai 448
                                                    fledg+l++r+++ +slde+ilr+v + fs+eGGl++++GnlGr+v+kvsav+ e++v+eapa+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 386 FLEDGELVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALENQVVEAPAM 449
                                                    **************************************************************** PP

                                      TIGR01196 449 vfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512
                                                    vf+dq++l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkvalvtdGr+s
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 450 VFQDQQDLADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMS 513
                                                    **************************************************************** PP

                                      TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednel 576
                                                    GasGk+paaihv+pea+ gGala++++Gd+ir+d+v+g le+ vd  e++ar++++  l  n++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 514 GASGKIPAAIHVSPEAYVGGALARVQEGDIIRVDGVKGTLELKVDAEEFAARTPAK-GLLGNNI 576
                                                    *****************************************************776.566789* PP

                                      TIGR01196 577 GlGrelfaalrekvssaeeGasslt 601
                                                    G+Grelf ++r + ssae+Gas++t
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 577 GTGRELFGFMRMAFSSAEQGASAFT 601
                                                    *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 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: 9.14
//
[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