Alignments for a candidate for edd in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Jannaschia aquimarina GSW-M26

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_043918138.1 jaqu_RS06435 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000877395.1:WP_043918138.1
          Length = 601

 Score =  681 bits (1758), Expect = 0.0
 Identities = 348/599 (58%), Positives = 442/599 (73%), Gaps = 10/599 (1%)

Query: 4   RVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLRMM 63
           R+ E+T+R+  RSR +REAYL  +R  A+ G +R  L C N AH  A  G E K +L   
Sbjct: 6   RIAEITDRIRDRSRDSREAYLKRMRDQAAQGVRRAHLACGNQAHAYAAMG-EQKDALVAD 64

Query: 64  NAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGME 123
              N+ IV++YNDMLSAHQP++ +P++IK A    G+  Q AGG PAMCDGVTQG+ GME
Sbjct: 65  RVPNIGIVTAYNDMLSAHQPFKDYPDRIKAAAARAGATAQVAGGVPAMCDGVTQGQTGME 124

Query: 124 LSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPS 183
           LSL SR+VIAL+T VALSHN FD+ L LGICDKIVPGL++ A  FG+LP IFVP GPM S
Sbjct: 125 LSLFSRDVIALATGVALSHNTFDSVLYLGICDKIVPGLVIAASTFGYLPGIFVPAGPMTS 184

Query: 184 GISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPG 243
           G+ N+EKA VR+ +AEGK  R++L+E+EM SYH PGTCTFYGTAN+NQ+LME MGLHLPG
Sbjct: 185 GLPNEEKARVRRDFAEGKVGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGLHLPG 244

Query: 244 ASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNH 303
           ASFVNP TPLRDALT  A ++ T +T     +TP+ +I+DE++ VN +V L ATGGSTN 
Sbjct: 245 ASFVNPGTPLRDALTDAATERATAITNLGNGYTPVCDILDEKAYVNGLVGLMATGGSTNL 304

Query: 304 TLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEA 363
            LH+ A+A+A+G++LT +D   +SE  P ++ VYPNG AD+NHF AAGG+ F+I  LL+A
Sbjct: 305 VLHLVAMARASGVRLTCEDFDAISEATPLMAKVYPNGLADVNHFHAAGGLPFMIGRLLDA 364

Query: 364 GLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVM 423
           GLLHEDV TVAG GLS Y  EP L +  L W+ GP E+L++ ILR V +AF+  GGLR M
Sbjct: 365 GLLHEDVRTVAGDGLSAYATEPKLGDDGLHWQPGPRETLNDRILRDVPQAFARTGGLREM 424

Query: 424 EGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNG 483
            GNLG GV KVSAVA +H+++EAPA +F DQ+++  AF+AGEL++D + V+RFQGP++NG
Sbjct: 425 RGNLGLGVTKVSAVAPEHRVIEAPARIFSDQEEVKAAFRAGELDRDVIVVVRFQGPKANG 484

Query: 484 MPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDI 543
           MPELH +TP L V+Q RG+KVALVTDGRMSGASGK+P+AIHV+PEA  GG LAR+RDGD+
Sbjct: 485 MPELHALTPPLSVVQGRGYKVALVTDGRMSGASGKVPSAIHVAPEAAAGGPLARLRDGDV 544

Query: 544 IRVDGVKGTL----ELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598
           IR D   GTL    E  +D D     +PA     N  G GRE+F   R   SSA+ GA+
Sbjct: 545 IRYDAEAGTLTCLTEGALDRDP-VPFDPAT----NAFGLGREMFETFRANVSSADTGAA 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: 1057
Number of extensions: 42
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_043918138.1 jaqu_RS06435 (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.4183442.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-290  948.1   0.1   9.3e-290  948.0   0.1    1.0  1  NCBI__GCF_000877395.1:WP_043918138.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000877395.1:WP_043918138.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  948.0   0.1  9.3e-290  9.3e-290       2     599 ..       5     599 ..       4     601 .] 0.99

  Alignments for each domain:
  == domain 1  score: 948.0 bits;  conditional E-value: 9.3e-290
                             TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 
                                           +r+aeit+ri +rs++ re+yl+++r+ + +g+ r++l+cgn ah++aa+ e +k +l  ++++n++i+tayn
  NCBI__GCF_000877395.1:WP_043918138.1   5 ARIAEITDRIRDRSRDSREAYLKRMRDQAAQGVRRAHLACGNQAHAYAAMGE-QKDALVADRVPNIGIVTAYN 76 
                                           79************************************************97.578999************** PP

                             TIGR01196  75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147
                                           dmlsahqpfk+ypd ik a+ +a+a+aqvagGvpamcdGvtqG+ Gmelsl+srdvial+t+++lshn fd+ 
  NCBI__GCF_000877395.1:WP_043918138.1  77 DMLSAHQPFKDYPDRIKAAAARAGATAQVAGGVPAMCDGVTQGQTGMELSLFSRDVIALATGVALSHNTFDSV 149
                                           ************************************************************************* PP

                             TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
                                           l+lG+cdkivpGl+iaa +fG lp++fvpaGpm+sGl+n+eka+vr++faeGkv+r++l+++emasyh+pGtc
  NCBI__GCF_000877395.1:WP_043918138.1 150 LYLGICDKIVPGLVIAASTFGYLPGIFVPAGPMTSGLPNEEKARVRRDFAEGKVGRDKLMEAEMASYHGPGTC 222
                                           ************************************************************************* PP

                             TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293
                                           tfyGtansnqml+e+mGlhlpgasfvnp tplrdalt +a++r++++t+ ++ ++p+++++dek+ vn+lvgl
  NCBI__GCF_000877395.1:WP_043918138.1 223 TFYGTANSNQMLMEFMGLHLPGASFVNPGTPLRDALTDAATERATAITNLGNGYTPVCDILDEKAYVNGLVGL 295
                                           ************************************************************************* PP

                             TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366
                                           +atGGstn  lhlva+ara+G+ l+ +d++++s+  pl+a+vypnG advnhf+aaGGl+f+i +ll++Gllh
  NCBI__GCF_000877395.1:WP_043918138.1 296 MATGGSTNLVLHLVAMARASGVRLTCEDFDAISEATPLMAKVYPNGLADVNHFHAAGGLPFMIGRLLDAGLLH 368
                                           ************************************************************************* PP

                             TIGR01196 367 edvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439
                                           edv+tvag Gl++y++ep+l d+ l++++++ ++l++ ilr v + f+ +GGl+ ++GnlG +v kvsav++e
  NCBI__GCF_000877395.1:WP_043918138.1 369 EDVRTVAGDGLSAYATEPKLGDDGLHWQPGPRETLNDRILRDVPQAFARTGGLREMRGNLGLGVTKVSAVAPE 441
                                           ************************************************************************* PP

                             TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512
                                           +rvieapa++f dq+e++aaf+agel+rd+++vvrfqGpkanGmpelh lt++l v+q rg+kvalvtdGr+s
  NCBI__GCF_000877395.1:WP_043918138.1 442 HRVIEAPARIFSDQEEVKAAFRAGELDRDVIVVVRFQGPKANGMPELHALTPPLSVVQGRGYKVALVTDGRMS 514
                                           ************************************************************************* PP

                             TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                           GasGkvp+aihv+pea++gG+la++rdGd+ir da +g l+ l + a    r +   d+  n +GlGre+f +
  NCBI__GCF_000877395.1:WP_043918138.1 515 GASGKVPSAIHVAPEAAAGGPLARLRDGDVIRYDAEAGTLTCLTEGAL--DRDPVPFDPATNAFGLGREMFET 585
                                           *******************************************98764..5778899**************** PP

                             TIGR01196 586 lrekvssaeeGass 599
                                           +r +vssa++Ga+ 
  NCBI__GCF_000877395.1:WP_043918138.1 586 FRANVSSADTGAAI 599
                                           ***********986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 37.15
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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