GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Paraburkholderia bryophila 376MFSha3.1

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate H281DRAFT_05315 H281DRAFT_05315 5-dehydro-4-deoxy-D-glucarate aldolase (EC 4.1.2.20)

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__Burk376:H281DRAFT_05315
          Length = 268

 Score =  323 bits (827), Expect = 3e-93
 Identities = 153/248 (61%), Positives = 192/248 (77%)

Query: 7   PNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALK 66
           PN F+ A+   +  IGCW++L++PI TE+LG+ GFDW++LD EHAPND+ T IPQLMALK
Sbjct: 13  PNSFRQAVRGGETLIGCWASLASPIVTELLGVIGFDWMLLDAEHAPNDVLTLIPQLMALK 72

Query: 67  GSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS 126
            S SAPVVR P N+ V+IKRLLD GF NFL+PFV++ ++A  AVA+TRYPP+GIRGVSV 
Sbjct: 73  DSRSAPVVRPPGNDSVVIKRLLDSGFSNFLVPFVDSADDAARAVAATRYPPQGIRGVSVG 132

Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186
           HR N + TV DYF  +N N+ ++VQIES+Q VD +D I A +GVDG+FVGPSDLAA  GH
Sbjct: 133 HRGNRYATVPDYFDIANDNVCVIVQIESRQAVDAIDEILAVDGVDGVFVGPSDLAAGYGH 192

Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246
           LGNA HPDVQ+AI H+F RA A GKPSGILAPV+ADA RY + G   +AV +DLG+ R+A
Sbjct: 193 LGNAGHPDVQQAIAHVFERAQAAGKPSGILAPVQADAERYRDMGCRIIAVCADLGLLRNA 252

Query: 247 TQKLADTF 254
            Q +   F
Sbjct: 253 AQTVHQHF 260


Lambda     K      H
   0.318    0.134    0.392 

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: 234
Number of extensions: 10
Number of successful extensions: 1
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: 256
Length of database: 268
Length adjustment: 25
Effective length of query: 231
Effective length of database: 243
Effective search space:    56133
Effective search space used:    56133
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: 47 (22.7 bits)

Align candidate H281DRAFT_05315 H281DRAFT_05315 (5-dehydro-4-deoxy-D-glucarate aldolase (EC 4.1.2.20))
to HMM TIGR03239 (garL: 2-dehydro-3-deoxyglucarate aldolase (EC 4.1.2.20))

# 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/TIGR03239.hmm
# target sequence database:        /tmp/gapView.28461.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03239  [M=249]
Accession:   TIGR03239
Description: GarL: 2-dehydro-3-deoxyglucarate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.9e-128  412.2   0.4   4.5e-128  412.0   0.4    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05315  H281DRAFT_05315 5-dehydro-4-deox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05315  H281DRAFT_05315 5-dehydro-4-deoxy-D-glucarate aldolase (EC 4.1.2.20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.0   0.4  4.5e-128  4.5e-128       1     248 [.      14     261 ..      14     262 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.0 bits;  conditional E-value: 4.5e-128
                                    TIGR03239   1 nrfrqkllarktliglwsalgnpitaevlglagfdwllldgehapndvltlipqlmalkdsasapv 66 
                                                  n frq++  ++tlig+w++l++pi +e+lg+ gfdw+lld+ehapndvltlipqlmalkds sapv
  lcl|FitnessBrowser__Burk376:H281DRAFT_05315  14 NSFRQAVRGGETLIGCWASLASPIVTELLGVIGFDWMLLDAEHAPNDVLTLIPQLMALKDSRSAPV 79 
                                                  88**************************************************************** PP

                                    TIGR03239  67 vrvplnepviikrlldigfynllipfvesaeeaeravaatryppegirgvsvaqrsnrygtvadyf 132
                                                  vr+p n+ v+ikrlld gf n+l+pfv+sa++a+ravaatrypp+girgvsv +r nry+tv+dyf
  lcl|FitnessBrowser__Burk376:H281DRAFT_05315  80 VRPPGNDSVVIKRLLDSGFSNFLVPFVDSADDAARAVAATRYPPQGIRGVSVGHRGNRYATVPDYF 145
                                                  ****************************************************************** PP

                                    TIGR03239 133 kkindnitvlvqiesrkgvdavdeiaavdgvdgvfvgpsdlaaalgylgnpnhpdvqkairhifdr 198
                                                     ndn++v+vqiesr+ vda+dei avdgvdgvfvgpsdlaa +g+lgn++hpdvq+ai h+f+r
  lcl|FitnessBrowser__Burk376:H281DRAFT_05315 146 DIANDNVCVIVQIESRQAVDAIDEILAVDGVDGVFVGPSDLAAGYGHLGNAGHPDVQQAIAHVFER 211
                                                  ****************************************************************** PP

                                    TIGR03239 199 aaahgkavgilapveadarrylelgatfvavgsdlgvfrsatkalsekfk 248
                                                  a+a+gk++gilapv+ada ry ++g +++av +dlg++r+a+++++++f 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05315 212 AQAAGKPSGILAPVQADAERYRDMGCRIIAVCADLGLLRNAAQTVHQHFM 261
                                                  ********************************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (268 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: 8.79
//
[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:

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