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

GapMind for catabolism of small carbon sources

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

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate Ac3H11_1866 L-asparaginase (EC 3.5.1.1)

Query= SwissProt::O68897
         (362 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1866
          Length = 362

 Score =  491 bits (1263), Expect = e-143
 Identities = 247/327 (75%), Positives = 282/327 (86%), Gaps = 1/327 (0%)

Query: 36  NVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQIANVRGEQVMQIASESI 95
           +VV+LATGGTIAGAGASAANSATY AAKV +++L+AG+PEL+ +A V GEQV QIASES 
Sbjct: 37  HVVVLATGGTIAGAGASAANSATYAAAKVPVDKLLAGLPELANVAKVSGEQVFQIASESF 96

Query: 96  NNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGT 155
            NE+LL+LG+RV+ L+   DVDGIVITHGTDTLEETAYFLNL  +T KPI+VVGSMRPGT
Sbjct: 97  TNEHLLRLGQRVSALSKQADVDGIVITHGTDTLEETAYFLNLTVRTTKPIVVVGSMRPGT 156

Query: 156 AMSADGMLNLYNAVAVAGSKDARGKGVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLG 215
           A+SADG LNLY+AV VA SKDA GKGVLVTMNDEIQSGRDVSK INIKTEAFKS WGPLG
Sbjct: 157 ALSADGALNLYDAVTVAASKDAAGKGVLVTMNDEIQSGRDVSKTINIKTEAFKSQWGPLG 216

Query: 216 MVVEGKSYWFRLPAKRHTMDSEFDIKTIKSLPDVEIAYGYGNVSDTAVKALAQAGAKAII 275
           MVVEGK+YWFR P KRHT  SEF+I  IK+LP V+I YGYGN++ T ++A  +AG KA+I
Sbjct: 217 MVVEGKNYWFRAPVKRHTTQSEFNIDDIKALPAVDIVYGYGNMNTTGIEAYGKAGVKALI 276

Query: 276 HAGTGNGSVSSKVVPALQELRKQGVQIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNP 335
           HAGTGNGSV+++ V +L+ LR  GVQIIRS+ V   GFVLRNAEQPDDKYDWVVAHDL P
Sbjct: 277 HAGTGNGSVAAQAVESLKALRASGVQIIRSARV-PDGFVLRNAEQPDDKYDWVVAHDLRP 335

Query: 336 QKARILAMVALTKTQDSKELQRMFWEY 362
           QKARILAMVALTKT DSKELQR+FWEY
Sbjct: 336 QKARILAMVALTKTNDSKELQRIFWEY 362


Lambda     K      H
   0.315    0.130    0.361 

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: 335
Number of extensions: 7
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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 (21.5 bits)
S2: 49 (23.5 bits)

Align candidate Ac3H11_1866 (L-asparaginase (EC 3.5.1.1))
to HMM TIGR00520 (L-asparaginase, type II (EC 3.5.1.1))

# 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/TIGR00520.hmm
# target sequence database:        /tmp/gapView.31562.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00520  [M=352]
Accession:   TIGR00520
Description: asnASE_II: L-asparaginase, type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.7e-120  386.6   1.6   5.6e-120  386.3   1.6    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866  L-asparaginase (EC 3.5.1.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866  L-asparaginase (EC 3.5.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.3   1.6  5.6e-120  5.6e-120      14     352 .]      25     362 .]      16     362 .] 0.97

  Alignments for each domain:
  == domain 1  score: 386.3 bits;  conditional E-value: 5.6e-120
                                        TIGR00520  14 lkvsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiege 75 
                                                      l++ a  +++ P++ +latGGtiag+g+s a+ a Y + k+ v++L+  +Pel+++a+++ge
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866  25 LSTVALAQAAKPHVVVLATGGTIAGAGASAANSATYAAAKVPVDKLLAGLPELANVAKVSGE 86 
                                                      55666678899*************************************************** PP

                                        TIGR00520  76 qivnvgsqdlneevllklakrisealasddvdGivithGtDtleetayfldltvksdkPvvl 137
                                                      q+ ++ s+++ +e+ll+l +r+s+  ++ dvdGivithGtDtleetayfl+ltv+++kP+v+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866  87 QVFQIASESFTNEHLLRLGQRVSALSKQADVDGIVITHGTDTLEETAYFLNLTVRTTKPIVV 148
                                                      ************************************************************** PP

                                        TIGR00520 138 vGamRpatsvsaDGplnLYnavsvaadeksagrGvlvvlndrilsarevtktnttsldtfks 199
                                                      vG+mRp t++saDG+lnLY+av+vaa++++ag+Gvlv++nd+i s+r+v kt   ++++fks
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 149 VGSMRPGTALSADGALNLYDAVTVAASKDAAGKGVLVTMNDEIQSGRDVSKTINIKTEAFKS 210
                                                      ************************************************************** PP

                                        TIGR00520 200 eeqGalGyiandkieyerepvkkhtletefdvskldeplPkvdiiYayqnlpeelvkavvda 261
                                                      +  G lG ++++k ++ r pvk+ht+++ef+++  +  lP vdi+Y+y n+ ++ ++a  +a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 211 Q-WGPLGMVVEGKNYWFRAPVKRHTTQSEFNIDDIKA-LPAVDIVYGYGNMNTTGIEAYGKA 270
                                                      9.*********************************99.************************ PP

                                        TIGR00520 262 gakGivlagvGnGslsaaalkvleeaakesvvivrssRvadGvvtkdae.vddkealiasgt 322
                                                      g k ++ ag+GnGs+ a+a++ l+ +  ++v i+rs Rv+dG v ++ae +ddk++ + +  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 271 GVKALIHAGTGNGSVAAQAVESLKALRASGVQIIRSARVPDGFVLRNAEqPDDKYDWVVAHD 332
                                                      *******************************************99876527888******** PP

                                        TIGR00520 323 LnPqkaRvLLqLaLtktkdlekiqevfeey 352
                                                      L PqkaR+L ++aLtkt+d +++q++f ey
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 333 LRPQKARILAMVALTKTNDSKELQRIFWEY 362
                                                      ***************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (362 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: 10.85
//
[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