Alignments for a candidate for garD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Acidovorax sp. GW101-3H11

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate Ac3H11_3953 D-galactarate dehydratase (EC 4.2.1.42)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3953
          Length = 525

 Score =  753 bits (1943), Expect = 0.0
 Identities = 372/518 (71%), Positives = 431/518 (83%), Gaps = 11/518 (2%)

Query: 16  IMMNDTDNVAIVVNDGGLPAGTVFPDG-----LTLVDRVPQGHKIALRDLKQGEAIVRYD 70
           I M+  DNVAIV NDGGLPAGTV P G     +TL D+VPQGHK+AL D+ +G+ + RY+
Sbjct: 8   IRMHPDDNVAIVANDGGLPAGTVLPPGVPGAGITLRDKVPQGHKVALSDMAEGDVVRRYN 67

Query: 71  VAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSV 130
           V IGYA++ IP G W+ E L+QMP AR L+ LP+AT KP    PL GYTFEGYRNADGSV
Sbjct: 68  VPIGYALKAIPAGSWVHERLLQMPSARALEGLPMATVKPPVLEPLTGYTFEGYRNADGSV 127

Query: 131 GTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGI 190
           GTRN+LAITTTVQCVAGVV +AV+RI+ ELLP YP V+DV+ LEHTYGCGVAIDAP+A I
Sbjct: 128 GTRNILAITTTVQCVAGVVANAVRRIKDELLPLYPQVDDVIGLEHTYGCGVAIDAPDAII 187

Query: 191 PIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGE----PYVVCLQDAE 246
           PIRTLRNISLNPNFGG+ MVVSLGCEKLQP+RLLP    PI  + +    P  VCLQ  E
Sbjct: 188 PIRTLRNISLNPNFGGEVMVVSLGCEKLQPDRLLPAGSFPIADERDAALGPETVCLQADE 247

Query: 247 HVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANPAVGFAT 306
           HVGF SM+D I+  A   L  LN RRRET  AS+LV+GVQCGGSDAFSGVTANPAVGF  
Sbjct: 248 HVGFMSMLDHIVQSARPHLERLNARRRETIRASELVLGVQCGGSDAFSGVTANPAVGFCA 307

Query: 307 DLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGVDRSANT 366
           DLLVRAGA+VMFSE TEVRD ++QLTSRA   EVA++++RE+ WYD YL +G VDR+ANT
Sbjct: 308 DLLVRAGATVMFSENTEVRDAVEQLTSRAATPEVAESIVRELGWYDRYLDRGRVDRAANT 367

Query: 367 TPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQ--QKGLIYAATPASDFICGTL 424
           TPGNK GGL+NI EKAMGSI+KSG++PIS VL+PG+KL+  Q+GL+YAATPASDFICGTL
Sbjct: 368 TPGNKAGGLSNIAEKAMGSIIKSGTAPISHVLAPGEKLRRDQRGLVYAATPASDFICGTL 427

Query: 425 QLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDV 484
           QLAAGMNLH+FTTGRGTPYGLA  PV+KVATR DLARRWHDLMD+NAG+IA GEASIE++
Sbjct: 428 QLAAGMNLHVFTTGRGTPYGLAECPVVKVATRTDLARRWHDLMDINAGKIADGEASIEEL 487

Query: 485 GWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522
           GWE+F L+LDVASG+K+TWAEQWKLHNAL LFNPAPVT
Sbjct: 488 GWEMFHLLLDVASGRKKTWAEQWKLHNALVLFNPAPVT 525


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: 908
Number of extensions: 40
Number of successful extensions: 4
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: 525
Length adjustment: 35
Effective length of query: 487
Effective length of database: 490
Effective search space:   238630
Effective search space used:   238630
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 Ac3H11_3953 (D-galactarate dehydratase (EC 4.2.1.42))
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.31626.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.9e-265  867.0   0.0   2.1e-265  866.8   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953  D-galactarate dehydratase (EC 4.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953  D-galactarate dehydratase (EC 4.2.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  866.8   0.0  2.1e-265  2.1e-265       1     507 []       6     525 .]       6     525 .] 0.97

  Alignments for each domain:
  == domain 1  score: 866.8 bits;  conditional E-value: 2.1e-265
                                        TIGR03248   1 lyirvneqdnvaivvndkGlpagtefe.....dgltlvekipqghkvalvdlekgdaiiryg 57 
                                                      l+ir++++dnvaiv+nd Glpagt+++     +g+tl++k+pqghkval d+++gd ++ry+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953   6 LTIRMHPDDNVAIVANDGGLPAGTVLPpgvpgAGITLRDKVPQGHKVALSDMAEGDVVRRYN 67 
                                                      689**********************98333335689************************** PP

                                        TIGR03248  58 eviGyavkdiarGswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGt 119
                                                        iGya+k+i+ Gswv+e+ll++psa ale lp+at +p+ l+pl GytfeGyrnadGsvGt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953  68 VPIGYALKAIPAGSWVHERLLQMPSARALEGLPMATVKPPVLEPLTGYTFEGYRNADGSVGT 129
                                                      ************************************************************** PP

                                        TIGR03248 120 knilgittsvqcvagvvdyavkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirt 181
                                                      +nil+itt+vqcvagvv  av+rik+ellp yp+vddv++l+h+yGcGvaidapdai+pirt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 130 RNILAITTTVQCVAGVVANAVRRIKDELLPLYPQVDDVIGLEHTYGCGVAIDAPDAIIPIRT 191
                                                      ************************************************************** PP

                                        TIGR03248 182 lrnlalnpnlGGealvvglGceklqperllpeelsa.velkdaav....lrlqdekl.Gfae 237
                                                      lrn++lnpn+GGe++vv+lGceklqp+rllp +  + +++ daa+    ++lq +++ Gf +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 192 LRNISLNPNFGGEVMVVSLGCEKLQPDRLLPAGSFPiADERDAALgpetVCLQADEHvGFMS 253
                                                      *******************************998875566666433333899988888**** PP

                                        TIGR03248 238 mveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGa 299
                                                      m+++i++ a+ +l++lnar+ret+ aselv+G+qcGGsdafsGvtanpavGf adllvraGa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 254 MLDHIVQSARPHLERLNARRRETIRASELVLGVQCGGSDAFSGVTANPAVGFCADLLVRAGA 315
                                                      ************************************************************** PP

                                        TIGR03248 300 tvlfsevtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGls 361
                                                      tv+fse+tevrda+++lt+ra++ eva++++re+ wyd+yl+rG++dr+anttpGnk GGls
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 316 TVMFSENTEVRDAVEQLTSRAATPEVAESIVRELGWYDRYLDRGRVDRAANTTPGNKAGGLS 377
                                                      ************************************************************** PP

                                        TIGR03248 362 nivekalGsivksGssaivevlspGekvk..kkGliyaatpasdfvcGtlqlasglnlhvft 421
                                                      ni eka+Gsi+ksG+++i++vl+pGek +  ++Gl+yaatpasdf+cGtlqla+g+nlhvft
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 378 NIAEKAMGSIIKSGTAPISHVLAPGEKLRrdQRGLVYAATPASDFICGTLQLAAGMNLHVFT 439
                                                      **************************9863379***************************** PP

                                        TIGR03248 422 tGrGtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwelfrlildvasG 483
                                                      tGrGtpyGla+ pv+kv+trt+la+rw+dl+d++aG+ia Gea+ie++Gwe+f+l+ldvasG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 440 TGRGTPYGLAECPVVKVATRTDLARRWHDLMDINAGKIADGEASIEELGWEMFHLLLDVASG 501
                                                      ************************************************************** PP

                                        TIGR03248 484 rkktwaekyklhndlalfnpapvt 507
                                                      rkktwae++klhn+l lfnpapvt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3953 502 RKKTWAEQWKLHNALVLFNPAPVT 525
                                                      ***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (525 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.28
//
[ok]

This GapMind analysis is from Sep 17 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:

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 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