Alignments for a candidate for edd in Phaeobacter inhibens BS107

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.31957.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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.43
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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