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.1961490.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: 00:00:00.01
# Mc/sec: 27.74
//
[ok]

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

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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:

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:

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:

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:

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