GapMind for Amino acid biosynthesis

 

Aligments for a candidate for carA in Escherichia coli BW25113

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate 14177 b0032 carbamoyl-phosphate synthase small subunit (NCBI)

Query= SwissProt::Q9LVW7
         (430 letters)



>lcl|FitnessBrowser__Keio:14177 b0032 carbamoyl-phosphate synthase
           small subunit (NCBI)
          Length = 382

 Score =  342 bits (878), Expect = 9e-99
 Identities = 177/381 (46%), Positives = 244/381 (64%), Gaps = 10/381 (2%)

Query: 57  NARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNT 116
           +A LVLEDG+ +  ++ GA G+ + E+VFNTS+TGYQEILTDPSY+ Q V +T P IGN 
Sbjct: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63

Query: 117 GVNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLR 176
           G N  DEES Q    GLVIR+L +  SN+R T+ L+ YL   +I+ + D+DTR +TR LR
Sbjct: 64  GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123

Query: 177 EDGSLIGVLSTEQSKTDDELLQMSRSWD-IVGIDLISDVSCKSPYEWVDKTNAEWDFNTN 235
           E G+  G +    +      L+ +R++  + G+DL  +V+    Y W   T   W     
Sbjct: 124 EKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSW---TQGSWTLTGG 180

Query: 236 SRDGKS-----YKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSN 290
             + K      + V+AYDFG K+NILR L   GC++T+VP+   A + LKMNPDGI  SN
Sbjct: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240

Query: 291 GPGDPSAVPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNN 349
           GPGDP+   YA+  +++ L   +PV+GIC+GHQLL  A G KT KMKFGHHGGNHPV++ 
Sbjct: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300

Query: 350 RTGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGP 409
               V I+AQNH +AVD A+LP  + VTH +L DG+  G+   +    S Q HPEASPGP
Sbjct: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360

Query: 410 HDSDNAFREFIELMKRSKQSS 430
           HD+   F  FIEL+++ ++++
Sbjct: 361 HDAAPLFDHFIELIEQYRKTA 381


Lambda     K      H
   0.316    0.134    0.403 

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: 458
Number of extensions: 20
Number of successful extensions: 3
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: 430
Length of database: 382
Length adjustment: 31
Effective length of query: 399
Effective length of database: 351
Effective search space:   140049
Effective search space used:   140049
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: 50 (23.9 bits)

Align candidate 14177 b0032 (carbamoyl-phosphate synthase small subunit (NCBI))
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

# 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.aa/TIGR01368.hmm
# target sequence database:        /tmp/gapView.3450.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01368  [M=361]
Accession:   TIGR01368
Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.1e-157  508.4   0.0   5.8e-157  508.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:14177  b0032 carbamoyl-phosphate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14177  b0032 carbamoyl-phosphate synthase small subunit (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.2   0.0  5.8e-157  5.8e-157       1     360 [.       5     375 ..       5     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 508.2 bits;  conditional E-value: 5.8e-157
                       TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvvk 79 
                                     a lvledGt+f+g+++ga++++vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ d+es++++++glv++
  lcl|FitnessBrowser__Keio:14177   5 ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTNDADEESSQVHAQGLVIR 83 
                                     579**************************************************************************** PP

                       TIGR01368  80 elskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvkevnlvkev 157
                                     +l   +sn+r++e+L+++lk+++ivai+++DTR+l++ lRekg+++++i + ++  +  + eka++ p +++++l+kev
  lcl|FitnessBrowser__Keio:14177  84 DLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLREKGAQNGCIIAGDNPdAALALEKARAFPGLNGMDLAKEV 162
                                     *************************************************999977345678999*************** PP

                       TIGR01368 158 stkeayeleq..........kakkegkk.lrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsnG 225
                                     +t+eay+++q          +akke++   +vv++d+G K+nilr+Lv+rg+++t+vpa+tsae++ k+npdgi+lsnG
  lcl|FitnessBrowser__Keio:14177 163 TTAEAYSWTQgswtltgglpEAKKEDELpFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNG 241
                                     *********98887766665466666667************************************************** PP

                       TIGR01368 226 PGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdees 304
                                     PGdPa +++ai+ ++k+le++iP+fGIclGhqllala+gakt+k+kfGh+G+Nhpvkd++++ v+it+qNHg+avde++
  lcl|FitnessBrowser__Keio:14177 242 PGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNVVMITAQNHGFAVDEAT 320
                                     ******************************************************************************* PP

                       TIGR01368 305 lkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                     l+++ l+vth++l+Dgt++g++++++p+fs Q HPeaspGphd++ lFd+f+eli+
  lcl|FitnessBrowser__Keio:14177 321 LPAN-LRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAAPLFDHFIELIE 375
                                     8866.************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (382 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.81
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or see changes to Amino acid biosynthesis since the publication.

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