Alignments for a candidate for edd in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Rhodobacter viridis JA737

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_110805670.1 C8J30_RS09805 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_003217355.1:WP_110805670.1
          Length = 606

 Score =  692 bits (1785), Expect = 0.0
 Identities = 357/599 (59%), Positives = 430/599 (71%), Gaps = 4/599 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  +  VT+R+ ARS A R  YLA I  A + GP R  L C N AH  A  G  DK  L
Sbjct: 8   LNATIARVTDRIRARSAARRGDYLARIAAAMAQGPARAHLACGNQAHAYAAMGP-DKAPL 66

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
                 N+ IV++YNDMLSAH PY  +P QIK ALR +G+  Q AGG PAMCDGVTQG A
Sbjct: 67  AEGRGPNIGIVTAYNDMLSAHAPYADYPAQIKAALRAIGATAQVAGGVPAMCDGVTQGRA 126

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIAL+  VALSH+ FDAA+ LG+CDKIVPGL+M A  FGHLP IF+P GP
Sbjct: 127 GMELSLFSRDVIALAAGVALSHDTFDAAIFLGVCDKIVPGLVMAAATFGHLPAIFLPAGP 186

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M +G+ N EKA VRQ++A G+  R++L+ +EM SYH PGTCTFYGTANTNQ+LMEVMGLH
Sbjct: 187 MTAGLPNDEKAKVRQQFATGEVGRDKLMAAEMASYHGPGTCTFYGTANTNQMLMEVMGLH 246

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP+TPLRDALT   A +V  +T    N  P+G ++DER+ VN +V L ATGGS
Sbjct: 247 LPGASFVNPHTPLRDALTVAGAHRVAAITALGENALPVGHLLDERAFVNGLVGLMATGGS 306

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  LH+PA+A+AAGI+L  +D  D+S  VP ++ VYPNG AD+N F AAGG+ FLIR L
Sbjct: 307 TNLVLHLPAMARAAGIELDLEDFDDISATVPLMAKVYPNGLADVNAFHAAGGLQFLIRHL 366

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L AGLLH DVNTVAG GL+RYTQ+  L  G+L W +GP +SL++ ILRP A  F+  GGL
Sbjct: 367 LRAGLLHADVNTVAGPGLARYTQDAKLIEGRLTWVEGPEDSLNDRILRPAATPFAATGGL 426

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           + + GNLGRGV+KVSAVA    ++EAPA VF+ Q  + DAFK GE  +D V V+RFQGP+
Sbjct: 427 KHLAGNLGRGVIKVSAVAPDRHVIEAPARVFESQDAVKDAFKRGEFTRDTVVVVRFQGPQ 486

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELH +TP L VLQDRG +VALVTDGRMSGASGK+PAAIHVSPEA  GG LAR+ D
Sbjct: 487 ANGMPELHSLTPTLSVLQDRGLRVALVTDGRMSGASGKVPAAIHVSPEAACGGPLARLLD 546

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPA-KGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598
           GD+IR+D   GTL    +   F  R PA   L  N  G GRELF   R     A  GAS
Sbjct: 547 GDLIRLDADTGTLTCLTEG--FETRAPATPDLSANRTGLGRELFETFRRNTGPATSGAS 603


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: 1083
Number of extensions: 48
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: 606
Length adjustment: 37
Effective length of query: 571
Effective length of database: 569
Effective search space:   324899
Effective search space used:   324899
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_110805670.1 C8J30_RS09805 (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.1755008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-287  940.8   0.9   1.6e-287  940.6   0.9    1.0  1  NCBI__GCF_003217355.1:WP_110805670.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110805670.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  940.6   0.9  1.6e-287  1.6e-287       2     600 ..      10     605 ..       9     606 .] 0.99

  Alignments for each domain:
  == domain 1  score: 940.6 bits;  conditional E-value: 1.6e-287
                             TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 
                                           + +a++t+ri +rs++ r  yl++i +a  +g+ r++l+cgn ah++aa+ + +k++l++ + +n++i+tayn
  NCBI__GCF_003217355.1:WP_110805670.1  10 ATIARVTDRIRARSAARRGDYLARIAAAMAQGPARAHLACGNQAHAYAAMGP-DKAPLAEGRGPNIGIVTAYN 81 
                                           5799**********************************************98.69****************** PP

                             TIGR01196  75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147
                                           dmlsah p+++yp++ik al+  +a+aqvagGvpamcdGvtqG++Gmelsl+srdvial+++++lsh+ fd+a
  NCBI__GCF_003217355.1:WP_110805670.1  82 DMLSAHAPYADYPAQIKAALRAIGATAQVAGGVPAMCDGVTQGRAGMELSLFSRDVIALAAGVALSHDTFDAA 154
                                           ************************************************************************* PP

                             TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
                                           +flGvcdkivpGl++aa++fGhlpa+f+paGpm++Gl+n+ekakvrq+fa G v+r++l+++emasyh+pGtc
  NCBI__GCF_003217355.1:WP_110805670.1 155 IFLGVCDKIVPGLVMAAATFGHLPAIFLPAGPMTAGLPNDEKAKVRQQFATGEVGRDKLMAAEMASYHGPGTC 227
                                           ************************************************************************* PP

                             TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293
                                           tfyGtan+nqml+e+mGlhlpgasfvnp+tplrdalt + a+r+a++ta +++ lp+++l+de+++vn+lvgl
  NCBI__GCF_003217355.1:WP_110805670.1 228 TFYGTANTNQMLMEVMGLHLPGASFVNPHTPLRDALTVAGAHRVAAITALGENALPVGHLLDERAFVNGLVGL 300
                                           ************************************************************************* PP

                             TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366
                                           +atGGstn  lhl a+araaGi l+ +d++++s  vpl+a+vypnG advn+f+aaGGl+flir+ll++Gllh
  NCBI__GCF_003217355.1:WP_110805670.1 301 MATGGSTNLVLHLPAMARAAGIELDLEDFDDISATVPLMAKVYPNGLADVNAFHAAGGLQFLIRHLLRAGLLH 373
                                           ************************************************************************* PP

                             TIGR01196 367 edvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439
                                            dv+tvag Gl ryt++++l +g+l++ e++e sl++ ilr++ +pf+a+GGlk l GnlGr+vikvsav+++
  NCBI__GCF_003217355.1:WP_110805670.1 374 ADVNTVAGPGLARYTQDAKLIEGRLTWVEGPEDSLNDRILRPAATPFAATGGLKHLAGNLGRGVIKVSAVAPD 446
                                           ************************************************************************* PP

                             TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512
                                            +vieapa+vf++q  +++afk+ge+ rd v+vvrfqGp+anGmpelh lt++l vlqdrg +valvtdGr+s
  NCBI__GCF_003217355.1:WP_110805670.1 447 RHVIEAPARVFESQDAVKDAFKRGEFTRDTVVVVRFQGPQANGMPELHSLTPTLSVLQDRGLRVALVTDGRMS 519
                                           ************************************************************************* PP

                             TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                           GasGkvpaaihv+pea+ gG+la++ dGdlirlda +g l+ l + +e  +r ++++dl++n+ GlGrelf +
  NCBI__GCF_003217355.1:WP_110805670.1 520 GASGKVPAAIHVSPEAACGGPLARLLDGDLIRLDADTGTLTCLTEGFE--TRAPATPDLSANRTGLGRELFET 590
                                           ********************************************9987..67788****************** PP

                             TIGR01196 586 lrekvssaeeGassl 600
                                           +r++++ a +Gas++
  NCBI__GCF_003217355.1:WP_110805670.1 591 FRRNTGPATSGASVI 605
                                           ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (606 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 17.16
//
[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)
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 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