GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Cupriavidus basilensis 4G11

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate RR42_RS26140 RR42_RS26140 glutaminase

Query= SwissProt::O68897
         (362 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS26140 RR42_RS26140 glutaminase
          Length = 373

 Score =  418 bits (1074), Expect = e-121
 Identities = 206/341 (60%), Positives = 264/341 (77%), Gaps = 1/341 (0%)

Query: 22  AAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQIAN 81
           AA A    ++ + AN+VI+ TGGTIAGAGA+A N+A YQ+A V ++++IA VPE+S+IAN
Sbjct: 34  AAGAPTQASEARKANIVIIGTGGTIAGAGAAATNTAAYQSAVVPVDKIIASVPEISKIAN 93

Query: 82  VRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKT 141
           V+GEQV QI SES NNE LL+LG+RV+EL    DVDGIVITHGTDT+EET YFLNL  K+
Sbjct: 94  VKGEQVFQIGSESFNNERLLKLGKRVSELLKQPDVDGIVITHGTDTIEETTYFLNLTLKS 153

Query: 142 DKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGKGVLVTMNDEIQSGRDVSKMIN 201
           DKP++VVGSMRPGTA+ ADG LNLY+AV VA S ++RGKG L  +NDEI +GRDV+K   
Sbjct: 154 DKPVVVVGSMRPGTALGADGALNLYDAVLVASSPESRGKGTLAVLNDEIHTGRDVTKSNT 213

Query: 202 IKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDIKTIKSLPDVEIAYGYGNVSDT 261
            K E F+SP+GPLG VVEG++ ++RLPA+ HTM +E+DI  I  LP+V + Y YGNV+  
Sbjct: 214 FKIETFRSPFGPLGYVVEGRTLYYRLPARPHTMQTEWDIDKIDKLPEVAVVYAYGNVNPA 273

Query: 262 AVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGVQIIRSSHVNAGGFVLRNAEQP 321
           ++ A  + GAKAI++A TGNGSV   +V  L+  R +GVQI+R+S    GG V+RNAEQP
Sbjct: 274 SIDAAVKNGAKAIVYAATGNGSVGDYMVEPLKAARAKGVQIVRASR-TGGGVVVRNAEQP 332

Query: 322 DDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFWEY 362
           DDKYDW+V  D  PQKARIL  +ALTKT D+KELQ++FW+Y
Sbjct: 333 DDKYDWLVTDDQLPQKARILMALALTKTNDTKELQKIFWKY 373


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: 325
Number of extensions: 8
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: 373
Length adjustment: 30
Effective length of query: 332
Effective length of database: 343
Effective search space:   113876
Effective search space used:   113876
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 RR42_RS26140 RR42_RS26140 (glutaminase)
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.14675.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-125  402.6   0.6   7.6e-125  402.3   0.6    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS26140  RR42_RS26140 glutaminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS26140  RR42_RS26140 glutaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.3   0.6  7.6e-125  7.6e-125      21     352 .]      43     373 .]      27     373 .] 0.95

  Alignments for each domain:
  == domain 1  score: 402.3 bits;  conditional E-value: 7.6e-125
                                 TIGR00520  21 aksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnvgsqdlneev 89 
                                               ++   ni i++tGGtiag+g+  ++ta+Y++ ++ v+++i +vPe+++ian++geq+ ++gs+++n+e 
  lcl|FitnessBrowser__Cup4G11:RR42_RS26140  43 EARKANIVIIGTGGTIAGAGAAATNTAAYQSAVVPVDKIIASVPEISKIANVKGEQVFQIGSESFNNER 111
                                               445579*************************************************************** PP

                                 TIGR00520  90 llklakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvsaDGplnLYna 158
                                               llkl kr+se l++ dvdGivithGtDt+eet yfl+lt+ksdkPvv+vG+mRp t++ aDG+lnLY+a
  lcl|FitnessBrowser__Cup4G11:RR42_RS26140 112 LLKLGKRVSELLKQPDVDGIVITHGTDTIEETTYFLNLTLKSDKPVVVVGSMRPGTALGADGALNLYDA 180
                                               ********************************************************************* PP

                                 TIGR00520 159 vsvaadeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtlet 227
                                               v va++++s+g+G+l vlnd+i  +r+vtk nt +++tf+s   G lGy++++ + y+r p+++ht++t
  lcl|FitnessBrowser__Cup4G11:RR42_RS26140 181 VLVASSPESRGKGTLAVLNDEIHTGRDVTKSNTFKIETFRSP-FGPLGYVVEGRTLYYRLPARPHTMQT 248
                                               *****************************************9.************************** PP

                                 TIGR00520 228 efdvskldeplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaakesvvivr 296
                                               e+d++k d+ lP+v ++Yay n+ ++ ++a+v++gak iv a++GnGs+ + +++ l+ a  ++v ivr
  lcl|FitnessBrowser__Cup4G11:RR42_RS26140 249 EWDIDKIDK-LPEVAVVYAYGNVNPASIDAAVKNGAKAIVYAATGNGSVGDYMVEPLKAARAKGVQIVR 316
                                               *********.*********************************************************** PP

                                 TIGR00520 297 ssRvadGvvtkdae.vddkealiasgtLnPqkaRvLLqLaLtktkdlekiqevfeey 352
                                               +sR+  Gvv ++ae +ddk++ +  +   PqkaR+L+ LaLtkt+d++++q++f +y
  lcl|FitnessBrowser__Cup4G11:RR42_RS26140 317 ASRTGGGVVVRNAEqPDDKYDWLVTDDQLPQKARILMALALTKTNDTKELQKIFWKY 373
                                               *******9998765277887766666667*************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (373 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: 7.84
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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