Alignments for a candidate for garD in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Collimonas pratensis Ter91

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate WP_061935898.1 CPter91_RS01210 galactarate dehydratase

Query= reanno::HerbieS:HSERO_RS15800
         (522 letters)



>NCBI__GCF_001584185.1:WP_061935898.1
          Length = 520

 Score =  852 bits (2200), Expect = 0.0
 Identities = 421/516 (81%), Positives = 462/516 (89%), Gaps = 4/516 (0%)

Query: 11  SAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYD 70
           + P YI M D DNVAIV NDGGLPAGT+FP GL L D+VPQGHK+ALRDL +GEAI+RY 
Sbjct: 5   AVPLYIRMQDEDNVAIVANDGGLPAGTIFPCGLVLRDKVPQGHKLALRDLAEGEAIIRYG 64

Query: 71  VAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSV 130
           VAIGYA R IP+G WIEESLV+MPPAREL NLPIAT+ P    PLEGYTFEGYRNADG+V
Sbjct: 65  VAIGYAQRAIPQGSWIEESLVRMPPARELSNLPIATRVPVAAAPLEGYTFEGYRNADGTV 124

Query: 131 GTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGI 190
           GTRN+LAI+TTVQCV+GVVEHAVKRI+AELL KYP+V+DV+ LEHTYGCGVAIDAP A I
Sbjct: 125 GTRNILAISTTVQCVSGVVEHAVKRIKAELLSKYPHVDDVIGLEHTYGCGVAIDAPGAEI 184

Query: 191 PIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPY----VVCLQDAE 246
           PIRTLRNIS+NPNFGGQAMVVSLGCEKLQP RL P+  IPI   G       VVCLQDAE
Sbjct: 185 PIRTLRNISMNPNFGGQAMVVSLGCEKLQPGRLFPQGTIPIQNTGGKEDGLRVVCLQDAE 244

Query: 247 HVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANPAVGFAT 306
           H+GF +MI SIM  AE +L+ELN RRRETCPAS+L VGVQCGGSDAFSGVTANPAVG+A+
Sbjct: 245 HIGFEAMIASIMATAEEQLSELNLRRRETCPASELTVGVQCGGSDAFSGVTANPAVGYAS 304

Query: 307 DLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGVDRSANT 366
           DLLVRAGA+VMFSE TEVRDGIDQLT+RA N EVA AMIREM WYD+YL +GGVDRSANT
Sbjct: 305 DLLVRAGATVMFSETTEVRDGIDQLTARAANPEVAAAMIREMAWYDDYLTRGGVDRSANT 364

Query: 367 TPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFICGTLQL 426
           TPGNKKGGLANIVEKAMGSIVKSGS PISGVLSPGDK++QKGLIYAATPASDF+CGTLQL
Sbjct: 365 TPGNKKGGLANIVEKAMGSIVKSGSRPISGVLSPGDKVRQKGLIYAATPASDFVCGTLQL 424

Query: 427 AAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDVGW 486
           AAGMNLH+FTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMD+NAGRIASGEA+IE+VGW
Sbjct: 425 AAGMNLHVFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDINAGRIASGEATIEEVGW 484

Query: 487 ELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522
           ELF+LMLDVASG+K+TWAE  KLHNALTLFNPAP+T
Sbjct: 485 ELFRLMLDVASGRKQTWAEHHKLHNALTLFNPAPIT 520


Lambda     K      H
   0.317    0.134    0.397 

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: 971
Number of extensions: 37
Number of successful extensions: 2
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: 522
Length of database: 520
Length adjustment: 35
Effective length of query: 487
Effective length of database: 485
Effective search space:   236195
Effective search space used:   236195
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_061935898.1 CPter91_RS01210 (galactarate dehydratase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

# 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/TIGR03248.hmm
# target sequence database:        /tmp/gapView.282619.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03248  [M=507]
Accession:   TIGR03248
Description: galactar-dH20: galactarate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-283  926.2   0.3   2.4e-283  926.0   0.3    1.0  1  NCBI__GCF_001584185.1:WP_061935898.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584185.1:WP_061935898.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  926.0   0.3  2.4e-283  2.4e-283       1     507 []       8     520 .]       8     520 .] 0.98

  Alignments for each domain:
  == domain 1  score: 926.0 bits;  conditional E-value: 2.4e-283
                             TIGR03248   1 lyirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGswv 73 
                                           lyir++++dnvaiv+nd Glpagt f++gl+l++k+pqghk+al dl++g+aiiryg  iGya+++i++Gsw+
  NCBI__GCF_001584185.1:WP_061935898.1   8 LYIRMQDEDNVAIVANDGGLPAGTIFPCGLVLRDKVPQGHKLALRDLAEGEAIIRYGVAIGYAQRAIPQGSWI 80 
                                           79*********************************************************************** PP

                             TIGR03248  74 keellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkrikke 146
                                           +e+l+++p a +l++lp+at+vp+++apleGytfeGyrnadG+vGt+nil+i t+vqcv+gvv++avkrik+e
  NCBI__GCF_001584185.1:WP_061935898.1  81 EESLVRMPPARELSNLPIATRVPVAAAPLEGYTFEGYRNADGTVGTRNILAISTTVQCVSGVVEHAVKRIKAE 153
                                           ************************************************************************* PP

                             TIGR03248 147 llpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllpeelsa.. 217
                                           ll kyp vddv++l+h+yGcGvaidap a +pirtlrn+++npn+GG+a+vv+lGceklqp rl+p+++++  
  NCBI__GCF_001584185.1:WP_061935898.1 154 LLSKYPHVDDVIGLEHTYGCGVAIDAPGAEIPIRTLRNISMNPNFGGQAMVVSLGCEKLQPGRLFPQGTIPiq 226
                                           *********************************************************************9954 PP

                             TIGR03248 218 ...velkdaavlrlqdekl.GfaemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpa 286
                                               +++   v++lqd+++ Gf++m+++i+++aee+l++ln r+ret+pasel+vG+qcGGsdafsGvtanpa
  NCBI__GCF_001584185.1:WP_061935898.1 227 ntgGKEDGLRVVCLQDAEHiGFEAMIASIMATAEEQLSELNLRRRETCPASELTVGVQCGGSDAFSGVTANPA 299
                                           4433345568********99***************************************************** PP

                             TIGR03248 287 vGfaadllvraGatvlfsevtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGG 359
                                           vG+a+dllvraGatv+fse+tevrd+i++lt+ra++ eva a+irem+wyd+yl+rG +drsanttpGnkkGG
  NCBI__GCF_001584185.1:WP_061935898.1 300 VGYASDLLVRAGATVMFSETTEVRDGIDQLTARAANPEVAAAMIREMAWYDDYLTRGGVDRSANTTPGNKKGG 372
                                           ************************************************************************* PP

                             TIGR03248 360 lsnivekalGsivksGssaivevlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlal 432
                                           l+niveka+GsivksGs +i++vlspG+kv++kGliyaatpasdfvcGtlqla+g+nlhvfttGrGtpyGla+
  NCBI__GCF_001584185.1:WP_061935898.1 373 LANIVEKAMGSIVKSGSRPISGVLSPGDKVRQKGLIYAATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAA 445
                                           ************************************************************************* PP

                             TIGR03248 433 vpvikvstrtelaerwadlidldaGriatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpap 505
                                           vpvikv+tr++la+rw+dl+d++aGria+Geatie+vGwelfrl+ldvasGrk+twae++klhn+l+lfnpap
  NCBI__GCF_001584185.1:WP_061935898.1 446 VPVIKVATRNDLARRWHDLMDINAGRIASGEATIEEVGWELFRLMLDVASGRKQTWAEHHKLHNALTLFNPAP 518
                                           ************************************************************************* PP

                             TIGR03248 506 vt 507
                                           +t
  NCBI__GCF_001584185.1:WP_061935898.1 519 IT 520
                                           *8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (520 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: 34.01
//
[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