GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Brucella inopinata BO1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_004689073.1 BIBO1_RS18110 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000182725.1:WP_004689073.1
          Length = 607

 Score =  738 bits (1906), Expect = 0.0
 Identities = 365/601 (60%), Positives = 455/601 (75%), Gaps = 2/601 (0%)

Query: 2   HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61
           H R+ E+TER+  RS+ TREAYL  +R AAS+ P+R  L CAN AHG A CG  DK +L 
Sbjct: 7   HKRIQEITERIRERSKPTREAYLDRVREAASNKPKRSFLGCANLAHGFAACGPHDKAALT 66

Query: 62  MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121
                N+ I+++YNDMLSAHQP+E FP+ IK+A RE G V Q AGG PAMCDGVTQG AG
Sbjct: 67  ADVVPNLGIITAYNDMLSAHQPFETFPQLIKQAAREAGGVAQVAGGVPAMCDGVTQGFAG 126

Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181
           MELSL SREVIA++TAV LSH+MFDAA+ LG+CDKIVPGL++GAL FGHLP +F+P GPM
Sbjct: 127 MELSLFSREVIAMATAVGLSHDMFDAAVYLGVCDKIVPGLIVGALTFGHLPAVFIPAGPM 186

Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            SG+ N EKA  RQ YAEGK  R ELLESE KSYH PGTCTFYGTAN+NQ+LME+MGLHL
Sbjct: 187 TSGLPNDEKAKTRQLYAEGKVGRAELLESESKSYHGPGTCTFYGTANSNQMLMEIMGLHL 246

Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301
           PGASF+NP TPLRDALT EAA++   +T     +TP+GE++DERS+VN +V L+ATGGST
Sbjct: 247 PGASFINPGTPLRDALTREAAKRALAITALGNEYTPVGEMIDERSIVNGVVGLNATGGST 306

Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361
           NHT+H+ A+A AAGI+LTW D++ +S+VVP L+ VYPNG AD+NHF AAGGM FLIRELL
Sbjct: 307 NHTIHLIAMAAAAGIKLTWHDISQISDVVPLLARVYPNGLADVNHFHAAGGMGFLIRELL 366

Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFL-DNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           + GLLHEDV TV G GL  Y  EP L  +G +V    P +S D+ +L  +A  F P GG+
Sbjct: 367 DGGLLHEDVRTVWGEGLRPYAIEPKLGPDGNVVREAAPEKSGDDKVLAKIAAPFQPTGGI 426

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           +V+ GN+G  ++KVSAV  +  ++EAPA VF DQ +L  AFKAG+L  DF+AV+R+QGP+
Sbjct: 427 KVLSGNIGNAIIKVSAVKPERHVIEAPAKVFNDQAELQAAFKAGDLTGDFIAVVRYQGPK 486

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELHK+   LG+LQDRG +VALVTDGR+SGASGK+P+AIHV+PEA  GG + ++R 
Sbjct: 487 ANGMPELHKLMTVLGILQDRGQRVALVTDGRLSGASGKVPSAIHVTPEALDGGMIGKIRT 546

Query: 541 GDIIRVDGVKGTLELKVDADEFAAR-EPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599
           GDIIR+D + GTLE+ ++     +R E    L GN  G GRELF   R     A++GAS 
Sbjct: 547 GDIIRLDAINGTLEVLLNQAVLDSRIEERPDLSGNEYGMGRELFRAFRQIAGRADEGASV 606

Query: 600 F 600
           F
Sbjct: 607 F 607


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: 46
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: 607
Length adjustment: 37
Effective length of query: 571
Effective length of database: 570
Effective search space:   325470
Effective search space used:   325470
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_004689073.1 BIBO1_RS18110 (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.678590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1054.2   0.2          0 1054.1   0.2    1.0  1  NCBI__GCF_000182725.1:WP_004689073.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000182725.1:WP_004689073.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1054.1   0.2         0         0       1     600 [.       7     607 .]       7     607 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1054.1 bits;  conditional E-value: 0
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h r++eiteri ersk+tre+yl+++r+a+++ ++rs lgc+nlahg+aa+ +++k++l+ + ++nl+iitay
  NCBI__GCF_000182725.1:WP_004689073.1   7 HKRIQEITERIRERSKPTREAYLDRVREAASNKPKRSFLGCANLAHGFAACGPHDKAALTADVVPNLGIITAY 79 
                                           689********************************************************************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahqpf+++p+lik+a++ea++vaqvagGvpamcdGvtqG +Gmelsl+sr+via++ta+glsh+mfd+
  NCBI__GCF_000182725.1:WP_004689073.1  80 NDMLSAHQPFETFPQLIKQAAREAGGVAQVAGGVPAMCDGVTQGFAGMELSLFSREVIAMATAVGLSHDMFDA 152
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           a++lGvcdkivpGl+++al+fGhlpavf+paGpm+sGl+n+ekak+rql+aeGkv+r ell+se++syh+pGt
  NCBI__GCF_000182725.1:WP_004689073.1 153 AVYLGVCDKIVPGLIVGALTFGHLPAVFIPAGPMTSGLPNDEKAKTRQLYAEGKVGRAELLESESKSYHGPGT 225
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtansnqml+e+mGlhlpgasf+np tplrdaltreaakr+ ++ta ++e++p++e+ide+sivn++vg
  NCBI__GCF_000182725.1:WP_004689073.1 226 CTFYGTANSNQMLMEIMGLHLPGASFINPGTPLRDALTREAAKRALAITALGNEYTPVGEMIDERSIVNGVVG 298
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           l atGGstnht+hl+a+a aaGi l+w+d+s++sd+vpllarvypnG advnhf+aaGG++flirell+ Gll
  NCBI__GCF_000182725.1:WP_004689073.1 299 LNATGGSTNHTIHLIAMAAAAGIKLTWHDISQISDVVPLLARVYPNGLADVNHFHAAGGMGFLIRELLDGGLL 371
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfle.dgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437
                                           hedv+tv g+Glr y++ep+l  dg+++++ a+eks d+++l+k+  pf+++GG+k+l+Gn+G a+ikvsavk
  NCBI__GCF_000182725.1:WP_004689073.1 372 HEDVRTVWGEGLRPYAIEPKLGpDGNVVREAAPEKSGDDKVLAKIAAPFQPTGGIKVLSGNIGNAIIKVSAVK 444
                                           *********************846************************************************* PP

                             TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510
                                           +e +vieapa+vf+dqael+aafkag+l +d++avvr+qGpkanGmpelhkl+tvlG+lqdrg++valvtdGr
  NCBI__GCF_000182725.1:WP_004689073.1 445 PERHVIEAPAKVFNDQAELQAAFKAGDLTGDFIAVVRYQGPKANGMPELHKLMTVLGILQDRGQRVALVTDGR 517
                                           ************************************************************************* PP

                             TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583
                                           lsGasGkvp+aihvtpeal+gG + kir+Gd+irlda+ng levl ++a l++r  e++dl+ ne+G+Grelf
  NCBI__GCF_000182725.1:WP_004689073.1 518 LSGASGKVPSAIHVTPEALDGGMIGKIRTGDIIRLDAINGTLEVLLNQAVLDSRIEERPDLSGNEYGMGRELF 590
                                           ************************************************************************* PP

                             TIGR01196 584 aalrekvssaeeGassl 600
                                            a+r++++ a+eGas++
  NCBI__GCF_000182725.1:WP_004689073.1 591 RAFRQIAGRADEGASVF 607
                                           **************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (607 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 33.88
//
[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