GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Phaeobacter inhibens BS107

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Phaeo:GFF2757
          Length = 607

 Score =  699 bits (1805), Expect = 0.0
 Identities = 349/606 (57%), Positives = 453/606 (74%), Gaps = 5/606 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  V +VT+R++ARS   R AYL  +R A   GP R  L C+  AH  A  G ED+  L
Sbjct: 3   LNQTVRDVTDRIIARSAKPRAAYLDRMRAAKGKGPARAHLSCSGQAHAYAATG-EDQMPL 61

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
               A ++ IV++YNDMLSAHQP+E +P++I+ A+R +G   Q AGG PAMCDGVTQGEA
Sbjct: 62  AEGTAGHLGIVTAYNDMLSAHQPFETYPQRIRDAVRRVGGTAQVAGGVPAMCDGVTQGEA 121

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+ IA++T +ALSHN+FDA + LG+CDKIVPGL++GA  FGHLP +F+P GP
Sbjct: 122 GMELSLFSRDTIAMATGIALSHNVFDATVYLGVCDKIVPGLVIGAQVFGHLPAVFLPAGP 181

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISN +KA VRQ++A G+  R+ELL+SEM +YH PGTCTFYGTANTNQ+LME MGLH
Sbjct: 182 MTSGISNDDKAKVRQKFAAGEIGRDELLKSEMAAYHGPGTCTFYGTANTNQMLMEFMGLH 241

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNP T +R ALT E A++   L+    ++TP+ +I+DER+ VN IV L  TGGS
Sbjct: 242 LPGSSFVNPGTDMRAALTEEGARRALALSALGNDYTPVCDILDERAYVNGIVGLMTTGGS 301

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  +H+ A+A+A GI L WQD ++LS+VVP L+ VYPNG AD+NHF AAGG+ ++I +L
Sbjct: 302 TNLLIHLIAMARAGGIILDWQDFSELSDVVPLLARVYPNGLADVNHFHAAGGLGYVIGQL 361

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L +G LH D  TVAG GL  YT EPFL +  LVW+ G  ESL++ I+RP +  F P GGL
Sbjct: 362 LNSGHLHSDTRTVAGSGLESYTAEPFLSDDGLVWKPGAAESLNDKIIRPASAPFQPTGGL 421

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEK-DFVAVMRFQGP 479
             + GNLG GVMK+SAVA +H++VEAPA VF DQ+++  AFKAGEL+K D + V+RFQGP
Sbjct: 422 ARLSGNLGTGVMKISAVAPEHRMVEAPARVFHDQEEVKAAFKAGELDKGDMIIVVRFQGP 481

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELH MTPFLG++Q RG KVALVTDGRMSGASGKIP+AIHV PEA  GG ++++R
Sbjct: 482 KANGMPELHSMTPFLGIMQGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGGPISKLR 541

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREP-AKGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598
           DGD++RVD + GTLE+K  A+ F  R+P    L     G+GRE+F   R A +SA+ GA+
Sbjct: 542 DGDMVRVDALTGTLEVK--AEGFDDRDPVVADLSAYQHGTGREMFALFRNAVTSADTGAT 599

Query: 599 AFTSAL 604
            F++ +
Sbjct: 600 VFSTLI 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: 1079
Number of extensions: 43
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: 608
Length of database: 607
Length adjustment: 37
Effective length of query: 571
Effective length of database: 570
Effective search space:   325470
Effective search space used:   325470
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 GFF2757 PGA1_c28000 (phosphogluconate dehydratase Edd)
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.13222.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.7e-288  943.1   0.5   3.1e-288  942.9   0.5    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2757  PGA1_c28000 phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2757  PGA1_c28000 phosphogluconate dehydratase Edd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  942.9   0.5  3.1e-288  3.1e-288       3     600 ..       6     601 ..       4     602 .. 0.99

  Alignments for each domain:
  == domain 1  score: 942.9 bits;  conditional E-value: 3.1e-288
                          TIGR01196   3 rlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmls 78 
                                         + ++t+rii+rs+k r +yl+++r+ak kg+ r++l+c+  ah++aa  e ++++l++ +  +l+i+tayndmls
  lcl|FitnessBrowser__Phaeo:GFF2757   6 TVRDVTDRIIARSAKPRAAYLDRMRAAKGKGPARAHLSCSGQAHAYAATGE-DQMPLAEGTAGHLGIVTAYNDMLS 80 
                                        5789*******************************************9886.689********************* PP

                          TIGR01196  79 ahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcd 154
                                        ahqpf++yp+ i++a+++ +++aqvagGvpamcdGvtqGe+Gmelsl+srd ia++t+i+lshn+fd++++lGvcd
  lcl|FitnessBrowser__Phaeo:GFF2757  81 AHQPFETYPQRIRDAVRRVGGTAQVAGGVPAMCDGVTQGEAGMELSLFSRDTIAMATGIALSHNVFDATVYLGVCD 156
                                        **************************************************************************** PP

                          TIGR01196 155 kivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnq 230
                                        kivpGl+i+a  fGhlpavf+paGpm+sG++n++kakvrq fa G ++r+ellksema+yh+pGtctfyGtan+nq
  lcl|FitnessBrowser__Phaeo:GFF2757 157 KIVPGLVIGAQVFGHLPAVFLPAGPMTSGISNDDKAKVRQKFAAGEIGRDELLKSEMAAYHGPGTCTFYGTANTNQ 232
                                        **************************************************************************** PP

                          TIGR01196 231 mlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhl 306
                                        ml+e+mGlhlpg+sfvnp t++r alt+e a+r+ +l a +++++p+++++de++ vn++vgl++tGGstn  +hl
  lcl|FitnessBrowser__Phaeo:GFF2757 233 MLMEFMGLHLPGSSFVNPGTDMRAALTEEGARRALALSALGNDYTPVCDILDERAYVNGIVGLMTTGGSTNLLIHL 308
                                        **************************************************************************** PP

                          TIGR01196 307 vaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytk 382
                                        +a+ara Giil+w+d+selsd+vpllarvypnG advnhf+aaGGl+++i +ll++G lh d++tvag+Gl+ yt 
  lcl|FitnessBrowser__Phaeo:GFF2757 309 IAMARAGGIILDWQDFSELSDVVPLLARVYPNGLADVNHFHAAGGLGYVIGQLLNSGHLHSDTRTVAGSGLESYTA 384
                                        **************************************************************************** PP

                          TIGR01196 383 epfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaella 458
                                        epfl+d+ l+++++a +sl+++i+r+++ pf+++GGl  l+GnlG +v+k+sav++e+r++eapa+vf+dq+e++a
  lcl|FitnessBrowser__Phaeo:GFF2757 385 EPFLSDDGLVWKPGAAESLNDKIIRPASAPFQPTGGLARLSGNLGTGVMKISAVAPEHRMVEAPARVFHDQEEVKA 460
                                        **************************************************************************** PP

                          TIGR01196 459 afkageler.dlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGa 533
                                        afkagel++ d+++vvrfqGpkanGmpelh +t++lG++q rg+kvalvtdGr+sGasGk+p+aihv peal+gG+
  lcl|FitnessBrowser__Phaeo:GFF2757 461 AFKAGELDKgDMIIVVRFQGPKANGMPELHSMTPFLGIMQGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGGP 536
                                        *******955****************************************************************** PP

                          TIGR01196 534 lakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                        + k+rdGd++r+da +g lev  + +  + r +   dl++ + G+Gre+fa +r++v+sa++Ga+++
  lcl|FitnessBrowser__Phaeo:GFF2757 537 ISKLRDGDMVRVDALTGTLEVKAEGF--DDRDPVVADLSAYQHGTGREMFALFRNAVTSADTGATVF 601
                                        ********************987765..6888999*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (607 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.53
//
[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