Alignments for a candidate for edd in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Marinobacter adhaerens HP15

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF2220 HP15_2174 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Marino:GFF2220
          Length = 610

 Score =  775 bits (2001), Expect = 0.0
 Identities = 380/601 (63%), Positives = 472/601 (78%), Gaps = 1/601 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHP V +VT+R++ RS  TR+ YL  +    +  P R  L C N AHG A C   DK +L
Sbjct: 5   MHPTVDKVTQRIIERSHPTRQDYLNRMNALKAQSPHRSSLSCGNLAHGFAACNQGDKDTL 64

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           + MN ANVA+V++YNDMLSAHQPYE FP+ I++A R MGSV Q AGGTPAMCDGVTQG+ 
Sbjct: 65  KFMNKANVAMVTAYNDMLSAHQPYEKFPDIIREAARGMGSVAQVAGGTPAMCDGVTQGQP 124

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+ IA+STAVALSHNMFDA L+LGICDKIVPGL++G+L FG+LPTI +P GP
Sbjct: 125 GMELSLFSRDTIAMSTAVALSHNMFDATLLLGICDKIVPGLLIGSLSFGYLPTILLPAGP 184

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSG+ NKEK  +RQ YAEGK  +EELLE+E KSYHSPGTCTFYGTAN+NQLL+EVMGLH
Sbjct: 185 MPSGLPNKEKQRIRQLYAEGKVGKEELLEAESKSYHSPGTCTFYGTANSNQLLVEVMGLH 244

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           +PG++FVNP TPLRD LT  A +QV RL+K  G    +G++VDE+S+VN++VAL  TGGS
Sbjct: 245 MPGSAFVNPNTPLRDELTRAATEQVIRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGS 304

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHT+H  AIA+AAGI + W D A+LS VVP+++ +YPNG+ D+N F  AGG  FLIREL
Sbjct: 305 TNHTIHWIAIARAAGIIIDWNDYAELSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIREL 364

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L  G +H DVNTV G GL RYT+ P L + +LVW+  P +SL  ++L PVA  F+P+GGL
Sbjct: 365 LSGGYVHNDVNTVVGYGLERYTEMPELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGL 424

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RV++GNLGRGV+KVSAVA +H+ VEAPAVVF DQ +L  AF+AG+L++D + ++RFQGP+
Sbjct: 425 RVLDGNLGRGVIKVSAVAPEHRKVEAPAVVFNDQNELKAAFEAGDLDRDCIVIVRFQGPK 484

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELHK+TP+LGVLQDRGFKV LVTDGRMSGASGK+PAAIHV PEA  GG LA+V++
Sbjct: 485 SNGMPELHKLTPYLGVLQDRGFKVGLVTDGRMSGASGKVPAAIHVYPEALDGGPLAKVKN 544

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKG-LLGNNVGSGRELFGFMRMAFSSAEQGASA 599
           GD++ +D   G L +++D  EFA RE  K  L G + G GRELFG+MR A S+ E+GAS 
Sbjct: 545 GDMVCLDAESGVLAIRLDDQEFAGRESEKADLTGYHHGYGRELFGWMRRAASNPEEGASF 604

Query: 600 F 600
           F
Sbjct: 605 F 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: 1099
Number of extensions: 44
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: 610
Length adjustment: 37
Effective length of query: 571
Effective length of database: 573
Effective search space:   327183
Effective search space used:   327183
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 GFF2220 HP15_2174 (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.13049.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.6e-298  974.7   0.0   8.6e-298  974.5   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2220  HP15_2174 6-phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2220  HP15_2174 6-phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  974.5   0.0  8.6e-298  8.6e-298       1     600 [.       6     605 ..       6     606 .. 0.99

  Alignments for each domain:
  == domain 1  score: 974.5 bits;  conditional E-value: 8.6e-298
                           TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                         h+ + ++t+riiers++tr+ yl+++++ k ++++rs+l+cgnlahg+aa+++ +k +lk ++++n+a++taynd
  lcl|FitnessBrowser__Marino:GFF2220   6 HPTVDKVTQRIIERSHPTRQDYLNRMNALKAQSPHRSSLSCGNLAHGFAACNQGDKDTLKFMNKANVAMVTAYND 80 
                                         68899********************************************************************** PP

                           TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150
                                         mlsahqp++++pd+i++a++  ++vaqvagG+pamcdGvtqG++Gmelsl+srd ia+sta++lshnmfd++l+l
  lcl|FitnessBrowser__Marino:GFF2220  81 MLSAHQPYEKFPDIIREAARGMGSVAQVAGGTPAMCDGVTQGQPGMELSLFSRDTIAMSTAVALSHNMFDATLLL 155
                                         *************************************************************************** PP

                           TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225
                                         G+cdkivpGlli++lsfG lp++++paGpm+sGl+nkek ++rql+aeGkv++eell++e++syh+pGtctfyGt
  lcl|FitnessBrowser__Marino:GFF2220 156 GICDKIVPGLLIGSLSFGYLPTILLPAGPMPSGLPNKEKQRIRQLYAEGKVGKEELLEAESKSYHSPGTCTFYGT 230
                                         *************************************************************************** PP

                           TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300
                                         ansnq+lve+mGlh+pg++fvnpntplrd+ltr+a++++ rl    g  l l++++deksivnalv+ll tGGst
  lcl|FitnessBrowser__Marino:GFF2220 231 ANSNQLLVEVMGLHMPGSAFVNPNTPLRDELTRAATEQVIRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGST 305
                                         ******************************************99999999************************* PP

                           TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375
                                         nht+h +aiaraaGii++w+d  els++vp ++r+ypnG+ dvn+f+ aGG +flirell+ G +h+dv+tv+g 
  lcl|FitnessBrowser__Marino:GFF2220 306 NHTIHWIAIARAAGIIIDWNDYAELSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIRELLSGGYVHNDVNTVVGY 380
                                         *************************************************************************** PP

                           TIGR01196 376 GlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivf 450
                                         Gl+ryt+ p l+d++l++++a+eksl  d+l +v +pf+++GGl++l+GnlGr+vikvsav++e+r++eapa+vf
  lcl|FitnessBrowser__Marino:GFF2220 381 GLERYTEMPELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGLRVLDGNLGRGVIKVSAVAPEHRKVEAPAVVF 455
                                         *************************************************************************** PP

                           TIGR01196 451 kdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvt 525
                                         +dq+el+aaf+ag+l+rd++++vrfqGpk+nGmpelhklt+ lGvlqdrgfkv lvtdGr+sGasGkvpaaihv 
  lcl|FitnessBrowser__Marino:GFF2220 456 NDQNELKAAFEAGDLDRDCIVIVRFQGPKSNGMPELHKLTPYLGVLQDRGFKVGLVTDGRMSGASGKVPAAIHVY 530
                                         *************************************************************************** PP

                           TIGR01196 526 pealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                         peal+gG+lak+++Gd++ lda +g l +  dd e++ re e+ dl   + G Grelf  +r+++s  eeGas +
  lcl|FitnessBrowser__Marino:GFF2220 531 PEALDGGPLAKVKNGDMVCLDAESGVLAIRLDDQEFAGRESEKADLTGYHHGYGRELFGWMRRAASNPEEGASFF 605
                                         ***********************************************************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (610 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: 00:00:00.04
# Mc/sec: 7.75
//
[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)
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