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 GFF1853 Psest_1892 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__psRCH2:GFF1853
          Length = 609

 Score =  977 bits (2526), Expect = 0.0
 Identities = 482/609 (79%), Positives = 545/609 (89%), Gaps = 1/609 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGS-EDKHS 59
           MHPRVLEVTERLV RSR TRE YLA++  AAS+GPQRG LQCANFAHGVAGC S +DK S
Sbjct: 1   MHPRVLEVTERLVERSRKTRERYLAMMAAAASEGPQRGGLQCANFAHGVAGCNSPQDKQS 60

Query: 60  LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119
           LR+MNA NVAIVS+YNDMLSAHQPYEHFPE I++ALRE+GSVGQFAGG PAMCDGVTQGE
Sbjct: 61  LRLMNAVNVAIVSAYNDMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGE 120

Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179
           AGME+SL SREVIA+STAVALSHNMFDAALMLGICDKIVPGLM+GALRFGHLPTIFVPGG
Sbjct: 121 AGMEMSLASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMIGALRFGHLPTIFVPGG 180

Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
           PMPSGI NK KA+VRQRYAEGKA+REELLESEMKSYHSPGTCTFYGTANTNQ++ME+MGL
Sbjct: 181 PMPSGIPNKAKAEVRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQVVMEIMGL 240

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299
           HLPG+SFVNPYTPLRDALT EAAQQVTRLT Q+GN+TP+ ++VDE+S+VNS+VAL+ATGG
Sbjct: 241 HLPGSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGG 300

Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359
           STNHTLH+PA A+AAGIQLTW+DMADLSEVVPTL+ VYPNG+AD+NHF A GG+ F++R 
Sbjct: 301 STNHTLHIPAFARAAGIQLTWKDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRT 360

Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           LL+AGLLHEDV+TV G+GL RY QEPFLD  +LVWRDGP +SLDE+ILRP  R FSPEGG
Sbjct: 361 LLDAGLLHEDVHTVVGKGLRRYIQEPFLDGDRLVWRDGPTQSLDESILRPAERPFSPEGG 420

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           LRV+EGNLGRGV K+SAVA +H++VEAPA VF DQ +LA AFKAGELE+DF+AV+RFQGP
Sbjct: 421 LRVLEGNLGRGVTKISAVAPEHRVVEAPARVFIDQSELAAAFKAGELERDFIAVVRFQGP 480

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGK+PAAIHV PEA  GG LARVR
Sbjct: 481 KANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVCPEALDGGPLARVR 540

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599
           DGDI+RVDG  G L   VD  E+ AREPA       +G GRELF FMR +FS+AEQGASA
Sbjct: 541 DGDILRVDGESGELLALVDPVEWGAREPAIRPEDVGIGCGRELFAFMRASFSTAEQGASA 600

Query: 600 FTSALENLK 608
           FT +LE L+
Sbjct: 601 FTESLEALR 609


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: 1230
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: 609
Length adjustment: 37
Effective length of query: 571
Effective length of database: 572
Effective search space:   326612
Effective search space used:   326612
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 GFF1853 Psest_1892 (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.2517.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 1036.7   0.0          0 1036.6   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1853  Psest_1892 6-phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1853  Psest_1892 6-phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1036.6   0.0         0         0       1     601 []       2     602 ..       2     602 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1036.6 bits;  conditional E-value: 0
                           TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaals.esekvelksekrknlaiitayn 74 
                                         h+r++e+ter++ers+ktre+yl+++ +a+++g++r+ l c+n+ahgva ++ +++k++l+ ++  n+ai++ayn
  lcl|FitnessBrowser__psRCH2:GFF1853   2 HPRVLEVTERLVERSRKTRERYLAMMAAAASEGPQRGGLQCANFAHGVAGCNsPQDKQSLRLMNAVNVAIVSAYN 76 
                                         79***********************************************9963799******************* PP

                           TIGR01196  75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalf 149
                                         dmlsahqp++++p++i++al+e ++v+q agGvpamcdGvtqGe+Gme+sl+sr+via+sta++lshnmfd+al+
  lcl|FitnessBrowser__psRCH2:GFF1853  77 DMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGEAGMEMSLASREVIAMSTAVALSHNMFDAALM 151
                                         *************************************************************************** PP

                           TIGR01196 150 lGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyG 224
                                         lG+cdkivpGl+i+al fGhlp++fvp+Gpm+sG++nk ka+vrq +aeGk++reell+sem+syh+pGtctfyG
  lcl|FitnessBrowser__psRCH2:GFF1853 152 LGICDKIVPGLMIGALRFGHLPTIFVPGGPMPSGIPNKAKAEVRQRYAEGKASREELLESEMKSYHSPGTCTFYG 226
                                         *************************************************************************** PP

                           TIGR01196 225 tansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGs 299
                                         tan+nq+++e+mGlhlpg+sfvnp+tplrdaltreaa++++rlt ++g+++pl++++deksivn++v+l atGGs
  lcl|FitnessBrowser__psRCH2:GFF1853 227 TANTNQVVMEIMGLHLPGSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGGS 301
                                         *************************************************************************** PP

                           TIGR01196 300 tnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvag 374
                                         tnhtlh+ a+araaGi+l+w+d+ +ls++vp+la+vypnG+advnhf+a+GG++f++r ll++Gllhedv+tv+g
  lcl|FitnessBrowser__psRCH2:GFF1853 302 TNHTLHIPAFARAAGIQLTWKDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRTLLDAGLLHEDVHTVVG 376
                                         *************************************************************************** PP

                           TIGR01196 375 kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaiv 449
                                         kGlrry +epfl+ ++l++r+++ +slde+ilr++++pfs+eGGl++l+GnlGr+v k+sav++e+rv+eapa+v
  lcl|FitnessBrowser__psRCH2:GFF1853 377 KGLRRYIQEPFLDGDRLVWRDGPTQSLDESILRPAERPFSPEGGLRVLEGNLGRGVTKISAVAPEHRVVEAPARV 451
                                         *************************************************************************** PP

                           TIGR01196 450 fkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihv 524
                                         f dq+el+aafkagelerd++avvrfqGpkanGmpelhklt++lGvlqdrg+kvalvtdGr+sGasGkvpaaihv
  lcl|FitnessBrowser__psRCH2:GFF1853 452 FIDQSELAAAFKAGELERDFIAVVRFQGPKANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHV 526
                                         *************************************************************************** PP

                           TIGR01196 525 tpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599
                                         +peal+gG+la++rdGd++r+d+ +gel  lvd +e+ are+  + +ed  +G+Grelfa++r   s+ae+Gas+
  lcl|FitnessBrowser__psRCH2:GFF1853 527 CPEALDGGPLARVRDGDILRVDGESGELLALVDPVEWGAREP-AIRPEDVGIGCGRELFAFMRASFSTAEQGASA 600
                                         *****************************************5.6899**************************99 PP

                           TIGR01196 600 lt 601
                                         +t
  lcl|FitnessBrowser__psRCH2:GFF1853 601 FT 602
                                         86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (609 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: 00:00:00.03
# Mc/sec: 9.85
//
[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