Alignments for a candidate for edd in Skermanella stibiiresistens SB22

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Skermanella stibiiresistens SB22

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_037452178.1 N825_RS13115 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000576635.1:WP_037452178.1
          Length = 608

 Score =  784 bits (2025), Expect = 0.0
 Identities = 386/601 (64%), Positives = 468/601 (77%), Gaps = 2/601 (0%)

Query: 5   VLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMN 64
           +  VT+R++ RS  TR AYLA IR AA  GP R +L C+N AHG A C ++DK  L    
Sbjct: 7   IARVTDRVIERSADTRAAYLARIRAAADKGPTRSRLSCSNLAHGFAACAADDKRDLADTV 66

Query: 65  AANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMEL 124
             ++AIVS+YNDMLSAHQP E+FP  IKKA+ E G V QFAGG PAMCDGVTQG AGMEL
Sbjct: 67  KPDIAIVSAYNDMLSAHQPLENFPAIIKKAVHENGGVAQFAGGVPAMCDGVTQGNAGMEL 126

Query: 125 SLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG 184
           SL SR+VIA++TAVALSH+MFD ALMLG+CDKI+PGL++GAL FGHLPTI VP GPM SG
Sbjct: 127 SLFSRDVIAMATAVALSHDMFDGALMLGVCDKIIPGLVIGALSFGHLPTIMVPAGPMTSG 186

Query: 185 ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGA 244
           + N EK+ +RQ YAEGK  RE LLE+E KSYH PGTCTFYGTAN+NQ+LME+MGLHLPGA
Sbjct: 187 LPNAEKSRIRQLYAEGKVGREALLEAESKSYHGPGTCTFYGTANSNQMLMEIMGLHLPGA 246

Query: 245 SFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHT 304
           +F+NP TPLRDALT  A++++  +T     + P GE+VDE++++N ++ L ATGGSTNHT
Sbjct: 247 AFINPNTPLRDALTAAASRRILEITALGNAYAPAGEVVDEKAVINGVIGLLATGGSTNHT 306

Query: 305 LHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAG 364
           +H+ A+AQ AGI+LTW D ADLS  VP L+ VYPNG AD+NHF AAGGMAF+IRELL+AG
Sbjct: 307 IHLIAMAQTAGIKLTWADFADLSAAVPLLAKVYPNGNADVNHFHAAGGMAFVIRELLDAG 366

Query: 365 LLHEDVNTVAG-RGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVM 423
           LLHEDV TVAG  G+ RY +EP  +  KL WR G   SLD  +L  VA  F+P+GG++V+
Sbjct: 367 LLHEDVLTVAGDGGMRRYAEEPVFEGEKLTWRPGTAVSLDRKVLGTVAEPFAPDGGIKVL 426

Query: 424 EGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNG 483
           +GN GR V+K SAV  +H+ VEAPA VF DQ +L  AFK GEL KDF+AV+ FQGP+SNG
Sbjct: 427 DGNFGRAVIKTSAVKHEHRFVEAPARVFTDQAELQAAFKRGELHKDFIAVVIFQGPKSNG 486

Query: 484 MPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDI 543
           MPELHK+TP LGVLQD+GFKVALVTDGRMSGASGK+PAAIHV+PEA  GG +A++RDGDI
Sbjct: 487 MPELHKLTPPLGVLQDQGFKVALVTDGRMSGASGKVPAAIHVTPEAASGGNIAKIRDGDI 546

Query: 544 IRVDGVKGTLELKVDADEFAAREP-AKGLLGNNVGSGRELFGFMRMAFSSAEQGASAFTS 602
           +R+D   G LE+ VDA+EFAAREP A  L GN  G+GR+LFG  R     AE GAS F +
Sbjct: 547 VRLDAEHGILEVLVDAEEFAAREPAAPDLTGNRFGTGRDLFGAFRAMVGGAEDGASVFNT 606

Query: 603 A 603
           A
Sbjct: 607 A 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: 1150
Number of extensions: 51
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: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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_037452178.1 N825_RS13115 (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.2725611.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 1021.5   1.4          0 1021.3   1.4    1.0  1  NCBI__GCF_000576635.1:WP_037452178.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000576635.1:WP_037452178.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.3   1.4         0         0       3     600 ..       6     604 ..       4     605 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1021.3 bits;  conditional E-value: 0
                             TIGR01196   3 rlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                            +a++t+r+iers++tr +yl++ir+a++kg+ rs+l+c+nlahg+aa++ ++k +l+ + ++++ai++aynd
  NCBI__GCF_000576635.1:WP_037452178.1   6 TIARVTDRVIERSADTRAAYLARIRAAADKGPTRSRLSCSNLAHGFAACAADDKRDLADTVKPDIAIVSAYND 78 
                                           589********************************************************************** PP

                             TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgal 148
                                           mlsahqp++++p++ikka++e+++vaq agGvpamcdGvtqG++Gmelsl+srdvia++ta++lsh+mfdgal
  NCBI__GCF_000576635.1:WP_037452178.1  79 MLSAHQPLENFPAIIKKAVHENGGVAQFAGGVPAMCDGVTQGNAGMELSLFSRDVIAMATAVALSHDMFDGAL 151
                                           ************************************************************************* PP

                             TIGR01196 149 flGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtct 221
                                           +lGvcdki+pGl+i+alsfGhlp+++vpaGpm+sGl+n ek+++rql+aeGkv+re+ll++e++syh+pGtct
  NCBI__GCF_000576635.1:WP_037452178.1 152 MLGVCDKIIPGLVIGALSFGHLPTIMVPAGPMTSGLPNAEKSRIRQLYAEGKVGREALLEAESKSYHGPGTCT 224
                                           ************************************************************************* PP

                             TIGR01196 222 fyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgll 294
                                           fyGtansnqml+e+mGlhlpga+f+npntplrdalt++a++r+ ++ta ++ + p++e++dek+++n+++gll
  NCBI__GCF_000576635.1:WP_037452178.1 225 FYGTANSNQMLMEIMGLHLPGAAFINPNTPLRDALTAAASRRILEITALGNAYAPAGEVVDEKAVINGVIGLL 297
                                           ************************************************************************* PP

                             TIGR01196 295 atGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhe 367
                                           atGGstnht+hl+a+a++aGi l+w d+ +ls  vplla+vypnG+advnhf+aaGG++f+irell++Gllhe
  NCBI__GCF_000576635.1:WP_037452178.1 298 ATGGSTNHTIHLIAMAQTAGIKLTWADFADLSAAVPLLAKVYPNGNADVNHFHAAGGMAFVIRELLDAGLLHE 370
                                           ************************************************************************* PP

                             TIGR01196 368 dvetvag.kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439
                                           dv tvag  G+rry++ep++e +kl++r+++  sld ++l +v +pf+++GG+k+l+Gn+Gravik+savk+e
  NCBI__GCF_000576635.1:WP_037452178.1 371 DVLTVAGdGGMRRYAEEPVFEGEKLTWRPGTAVSLDRKVLGTVAEPFAPDGGIKVLDGNFGRAVIKTSAVKHE 443
                                           ******9568*************************************************************** PP

                             TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512
                                           +r +eapa+vf dqael+aafk+gel++d++avv fqGpk+nGmpelhklt++lGvlqd+gfkvalvtdGr+s
  NCBI__GCF_000576635.1:WP_037452178.1 444 HRFVEAPARVFTDQAELQAAFKRGELHKDFIAVVIFQGPKSNGMPELHKLTPPLGVLQDQGFKVALVTDGRMS 516
                                           ************************************************************************* PP

                             TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                           GasGkvpaaihvtpea++gG++akirdGd++rlda  g levlvd  e++are++ +dl  n++G+Gr+lf a
  NCBI__GCF_000576635.1:WP_037452178.1 517 GASGKVPAAIHVTPEAASGGNIAKIRDGDIVRLDAEHGILEVLVDAEEFAAREPAAPDLTGNRFGTGRDLFGA 589
                                           ************************************************************************* PP

                             TIGR01196 586 lrekvssaeeGassl 600
                                           +r +v++ae+Gas++
  NCBI__GCF_000576635.1:WP_037452178.1 590 FRAMVGGAEDGASVF 604
                                           ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 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: 29.76
//
[ok]

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

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Steps (tab-delimited)
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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