Alignments for a candidate for edd in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Rhodobacter johrii JA192

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_069330746.1 C8J29_RS04890 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_003046325.1:WP_069330746.1
          Length = 601

 Score =  696 bits (1796), Expect = 0.0
 Identities = 352/599 (58%), Positives = 435/599 (72%), Gaps = 4/599 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  V  VT+R+ ARS A+R AYL     AA  GP R  L C N AH  A  G EDK +L
Sbjct: 3   LNATVARVTDRIRARSEASRSAYLERTGRAAEAGPVRAHLTCGNQAHAYAAMG-EDKEAL 61

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
               A N+ IV++YNDMLSAHQPYE +P  I+ A R  G+  Q AGG PAMCDGVTQG+ 
Sbjct: 62  AAGRAPNLGIVTAYNDMLSAHQPYEDYPRLIRAAARRAGATAQVAGGVPAMCDGVTQGQP 121

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIAL+  V+LSHN +DAAL LGICDKIVPGL+M A  FGH+P +FVPGGP
Sbjct: 122 GMELSLFSRDVIALAAGVSLSHNCYDAALFLGICDKIVPGLVMAAATFGHVPAVFVPGGP 181

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SG+ N EK+ VR ++A G+  R+ L+ +EM SYH PGTCTFYGTANTNQ+LME MGLH
Sbjct: 182 MTSGLPNDEKSRVRNQFATGEVGRDALMAAEMASYHGPGTCTFYGTANTNQMLMEFMGLH 241

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLR+ALT  A ++   +T    ++ P+ +I+DER+ VN +V L ATGGS
Sbjct: 242 LPGASFVNPNTPLREALTVAAVERAAAITALGNDYRPVAQILDERAFVNGLVGLMATGGS 301

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  LH+PA+A+AAG+ L  +D AD+SE VP ++ VYPNG AD+NHF AAGG+ ++I +L
Sbjct: 302 TNLVLHLPAMARAAGVILDLEDFADISEAVPLMAKVYPNGMADVNHFHAAGGLPYMIGQL 361

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+AGLLHE+V TVAG GLS Y +EP L    LVWRDGP  S ++ ILRP    F P GGL
Sbjct: 362 LDAGLLHEEVQTVAGEGLSLYRREPVLTEEGLVWRDGPEASQNDRILRPATDPFQPSGGL 421

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           R + GNLGRGVMKVSAVA    ++EAPA +F DQ+ +  AF+AGE   D V V+RFQGPR
Sbjct: 422 RQLSGNLGRGVMKVSAVAPDRHVIEAPARIFHDQEAVKAAFRAGEFTSDTVVVVRFQGPR 481

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELH +TP L VLQDRG +VALVTDGRMSGASGK+P+AIHV+PEA +GG LAR+RD
Sbjct: 482 ANGMPELHSLTPVLSVLQDRGLRVALVTDGRMSGASGKVPSAIHVAPEAAMGGPLARLRD 541

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNV-GSGRELFGFMRMAFSSAEQGAS 598
           GD++RVD   G L+  V A+ F  R P +  L  +  G GRELF   R    S+ +GA+
Sbjct: 542 GDLLRVDATAGRLD--VLAEGFEDRAPVEADLSASAHGIGRELFAAFRATVGSSTEGAA 598


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: 1093
Number of extensions: 44
Number of successful extensions: 3
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: 601
Length adjustment: 37
Effective length of query: 571
Effective length of database: 564
Effective search space:   322044
Effective search space used:   322044
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 WP_069330746.1 C8J29_RS04890 (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.1330305.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.6e-291  951.2   0.7   1.1e-290  951.0   0.7    1.0  1  NCBI__GCF_003046325.1:WP_069330746.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003046325.1:WP_069330746.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  951.0   0.7  1.1e-290  1.1e-290       2     600 ..       5     600 ..       4     601 .] 0.99

  Alignments for each domain:
  == domain 1  score: 951.0 bits;  conditional E-value: 1.1e-290
                             TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 
                                           + +a++t+ri +rs++ r++yle+   a++ g++r++l+cgn ah++aa+ e +k +l+  + +nl+i+tayn
  NCBI__GCF_003046325.1:WP_069330746.1   5 ATVARVTDRIRARSEASRSAYLERTGRAAEAGPVRAHLTCGNQAHAYAAMGE-DKEALAAGRAPNLGIVTAYN 76 
                                           5689**********************************************96.6899**************** PP

                             TIGR01196  75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147
                                           dmlsahqp+++yp li+ a+++a+a+aqvagGvpamcdGvtqG++Gmelsl+srdvial+++++lshn +d+a
  NCBI__GCF_003046325.1:WP_069330746.1  77 DMLSAHQPYEDYPRLIRAAARRAGATAQVAGGVPAMCDGVTQGQPGMELSLFSRDVIALAAGVSLSHNCYDAA 149
                                           ************************************************************************* PP

                             TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
                                           lflG+cdkivpGl++aa++fGh+pavfvp+Gpm+sGl+n+ek++vr++fa G v+r++l+++emasyh+pGtc
  NCBI__GCF_003046325.1:WP_069330746.1 150 LFLGICDKIVPGLVMAAATFGHVPAVFVPGGPMTSGLPNDEKSRVRNQFATGEVGRDALMAAEMASYHGPGTC 222
                                           ************************************************************************* PP

                             TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293
                                           tfyGtan+nqml+e+mGlhlpgasfvnpntplr+alt +a +r+a++ta ++++ p+a+++de+++vn+lvgl
  NCBI__GCF_003046325.1:WP_069330746.1 223 TFYGTANTNQMLMEFMGLHLPGASFVNPNTPLREALTVAAVERAAAITALGNDYRPVAQILDERAFVNGLVGL 295
                                           ************************************************************************* PP

                             TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366
                                           +atGGstn  lhl a+araaG+il+ +d+ ++s+ vpl+a+vypnG advnhf+aaGGl+++i +ll++Gllh
  NCBI__GCF_003046325.1:WP_069330746.1 296 MATGGSTNLVLHLPAMARAAGVILDLEDFADISEAVPLMAKVYPNGMADVNHFHAAGGLPYMIGQLLDAGLLH 368
                                           ************************************************************************* PP

                             TIGR01196 367 edvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439
                                           e+v+tvag+Gl+ y +ep+l+++ l++r+++e+s ++ ilr++ +pf+++GGl+ l+GnlGr+v+kvsav+++
  NCBI__GCF_003046325.1:WP_069330746.1 369 EEVQTVAGEGLSLYRREPVLTEEGLVWRDGPEASQNDRILRPATDPFQPSGGLRQLSGNLGRGVMKVSAVAPD 441
                                           ************************************************************************* PP

                             TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512
                                            +vieapa++f+dq+ ++aaf+age+  d v+vvrfqGp+anGmpelh lt+vl vlqdrg +valvtdGr+s
  NCBI__GCF_003046325.1:WP_069330746.1 442 RHVIEAPARIFHDQEAVKAAFRAGEFTSDTVVVVRFQGPRANGMPELHSLTPVLSVLQDRGLRVALVTDGRMS 514
                                           ************************************************************************* PP

                             TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                           GasGkvp+aihv+pea++gG+la++rdGdl+r+da++g+l+vl + +e   r + e dl+++  G+Grelfaa
  NCBI__GCF_003046325.1:WP_069330746.1 515 GASGKVPSAIHVAPEAAMGGPLARLRDGDLLRVDATAGRLDVLAEGFED--RAPVEADLSASAHGIGRELFAA 585
                                           ********************************************99875..566699**************** PP

                             TIGR01196 586 lrekvssaeeGassl 600
                                           +r +v+s+ eGa+++
  NCBI__GCF_003046325.1:WP_069330746.1 586 FRATVGSSTEGAAVV 600
                                           ***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (601 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: 00:00:00.01
# Mc/sec: 25.36
//
[ok]

This GapMind analysis is from Sep 24 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)
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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 2024 update 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