Alignments for a candidate for edd in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas stutzeri RCH2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF835 Psest_0849 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__psRCH2:GFF835
          Length = 608

 Score =  952 bits (2462), Expect = 0.0
 Identities = 471/608 (77%), Positives = 536/608 (88%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHP V+EVTERL+ RSR TREAYLA+IRGAAS GP R   QCANFAHGVAGCG++DK  L
Sbjct: 1   MHPVVVEVTERLIQRSRPTREAYLAMIRGAASAGPARNGAQCANFAHGVAGCGTQDKQRL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R+ +AANVAIV++YNDMLSAHQPYE +PE++++ALR++GSVGQ AGG PAMCDGVTQGE 
Sbjct: 61  RLPDAANVAIVTAYNDMLSAHQPYEGYPERLRQALRDVGSVGQVAGGVPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMEL++ SREVIA+STAVALSHN+FDAAL+LGICDKIVPGL++GALRFGHLP +FVP GP
Sbjct: 121 GMELAIASREVIAMSTAVALSHNLFDAALLLGICDKIVPGLLIGALRFGHLPAVFVPAGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSG++NK+KA VRQRYAEGKA+R+ELL +EM++YHSPGTCTFYGTANTNQ+LMEVMGLH
Sbjct: 181 MPSGLANKDKAAVRQRYAEGKASRDELLAAEMQAYHSPGTCTFYGTANTNQMLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNP TPLRDALT EAA+QVTRLT Q G FTP+GE+VDER LVN+IVALHATGGS
Sbjct: 241 LPGSSFVNPGTPLRDALTAEAARQVTRLTPQGGCFTPLGELVDERVLVNAIVALHATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLHMPAIAQAAGIQLTWQDMADLS VVPTL+ VYPNG ADINHF AAGG+A L+REL
Sbjct: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSAVVPTLARVYPNGPADINHFHAAGGVAVLVREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L AGLLHEDV+TV GRGLSRYTQEPFL+ G+L WR+G   SLDE++LRPVAR FS EGGL
Sbjct: 361 LAAGLLHEDVHTVMGRGLSRYTQEPFLEGGRLTWREGAAASLDESLLRPVARPFSAEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVM GNLGRGVMKVSAVA +H++VEAPA VF DQ +L +AFKAGELE+D VAV+RFQGPR
Sbjct: 421 RVMSGNLGRGVMKVSAVAPEHRVVEAPARVFADQLELVEAFKAGELERDVVAVVRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELHK+TP+LG+LQDRGFKVALVTDGRMSGASGK+PAAIHV PEA  GG LARVRD
Sbjct: 481 ANGMPELHKLTPYLGLLQDRGFKVALVTDGRMSGASGKVPAAIHVCPEAIDGGPLARVRD 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GD++RVDG  G LE+ VDA E A R P      +  G GRELFGFMR AFSSAEQGAS F
Sbjct: 541 GDLLRVDGQAGVLEVLVDAAELAGRSPVAAPAASVQGCGRELFGFMRSAFSSAEQGASVF 600

Query: 601 TSALENLK 608
           T+ LE L+
Sbjct: 601 TAGLEALR 608


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: 1284
Number of extensions: 55
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 GFF835 Psest_0849 (6-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.20593.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 1023.9   0.2          0 1023.7   0.2    1.0  1  lcl|FitnessBrowser__psRCH2:GFF835  Psest_0849 6-phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF835  Psest_0849 6-phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1023.7   0.2         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1023.7 bits;  conditional E-value: 0
                          TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndm 76 
                                        h+ ++e+ter+i+rs++tre+yl++ir a++ g+ r+   c+n+ahgva +  ++k+ l+    +n+ai+tayndm
  lcl|FitnessBrowser__psRCH2:GFF835   2 HPVVVEVTERLIQRSRPTREAYLAMIRGAASAGPARNGAQCANFAHGVAGCGTQDKQRLRLPDAANVAIVTAYNDM 77 
                                        67799*********************************************************************** PP

                          TIGR01196  77 lsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGv 152
                                        lsahqp++ yp+ +++al++ ++v+qvagGvpamcdGvtqGe+Gmel+++sr+via+sta++lshn+fd+al+lG+
  lcl|FitnessBrowser__psRCH2:GFF835  78 LSAHQPYEGYPERLRQALRDVGSVGQVAGGVPAMCDGVTQGEPGMELAIASREVIAMSTAVALSHNLFDAALLLGI 153
                                        **************************************************************************** PP

                          TIGR01196 153 cdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtans 228
                                        cdkivpGlli+al fGhlpavfvpaGpm+sGl nk+ka+vrq +aeGk++r+ell++em++yh+pGtctfyGtan+
  lcl|FitnessBrowser__psRCH2:GFF835 154 CDKIVPGLLIGALRFGHLPAVFVPAGPMPSGLANKDKAAVRQRYAEGKASRDELLAAEMQAYHSPGTCTFYGTANT 229
                                        **************************************************************************** PP

                          TIGR01196 229 nqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtl 304
                                        nqml+e+mGlhlpg+sfvnp tplrdalt+eaa++++rlt+++g ++pl+el+de+++vna+v+l+atGGstnhtl
  lcl|FitnessBrowser__psRCH2:GFF835 230 NQMLMEVMGLHLPGSSFVNPGTPLRDALTAEAARQVTRLTPQGGCFTPLGELVDERVLVNAIVALHATGGSTNHTL 305
                                        **************************************************************************** PP

                          TIGR01196 305 hlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrry 380
                                        h+ aia+aaGi+l+w+d+ +ls +vp+larvypnG ad+nhf+aaGG+++l+rell +Gllhedv+tv+g+Gl+ry
  lcl|FitnessBrowser__psRCH2:GFF835 306 HMPAIAQAAGIQLTWQDMADLSAVVPTLARVYPNGPADINHFHAAGGVAVLVRELLAAGLLHEDVHTVMGRGLSRY 381
                                        **************************************************************************** PP

                          TIGR01196 381 tkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqael 456
                                        t+epfle g+l++re+a +slde++lr+v +pfsaeGGl++++GnlGr+v+kvsav++e+rv+eapa+vf dq el
  lcl|FitnessBrowser__psRCH2:GFF835 382 TQEPFLEGGRLTWREGAAASLDESLLRPVARPFSAEGGLRVMSGNLGRGVMKVSAVAPEHRVVEAPARVFADQLEL 457
                                        **************************************************************************** PP

                          TIGR01196 457 laafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegG 532
                                        ++afkagelerd+vavvrfqGp+anGmpelhklt+ lG+lqdrgfkvalvtdGr+sGasGkvpaaihv+pea++gG
  lcl|FitnessBrowser__psRCH2:GFF835 458 VEAFKAGELERDVVAVVRFQGPRANGMPELHKLTPYLGLLQDRGFKVALVTDGRMSGASGKVPAAIHVCPEAIDGG 533
                                        **************************************************************************** PP

                          TIGR01196 533 alakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601
                                        +la++rdGdl+r+d+++g levlvd ael+ r++   ++ ++ +G+Grelf ++r++ ssae+Gas++t
  lcl|FitnessBrowser__psRCH2:GFF835 534 PLARVRDGDLLRVDGQAGVLEVLVDAAELAGRSP-VAAPAASVQGCGRELFGFMRSAFSSAEQGASVFT 601
                                        ********************************96.56789999***********************986 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.37
//
[ok]

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

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Steps (tab-delimited)
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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