GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Caulobacter crescentus NA1000

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate CCNA_02925 CCNA_02925 carbamoyl-phosphate synthase small chain

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Caulo:CCNA_02925
          Length = 388

 Score =  376 bits (966), Expect = e-109
 Identities = 195/379 (51%), Positives = 248/379 (65%), Gaps = 10/379 (2%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           + +L L DG    G   GA G AVGEV FNT+MTGYQEILTDPSY  QIV  T+PH+GNV
Sbjct: 10  TGVLALADGAILQGVGCGAVGDAVGEVCFNTAMTGYQEILTDPSYMAQIVAFTFPHVGNV 69

Query: 64  GTNDADEES----SQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119
           G N  D E     ++  A+G + RD+P + +N+R   D  +++K   +V +A +DTR LT
Sbjct: 70  GVNGEDVEQITGVAETAARGALFRDVPTVQANWRADGDFDAWMKARGVVGLAGVDTRALT 129

Query: 120 RLLREKGAQNGCIIAGDNP--DAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTL 177
           R +RE G  +G I    +   D A  + KA+A+ GL G+DLAK+ +T + ++W +G W+ 
Sbjct: 130 RKIRETGMPHGVIAHSPDGQFDLAALVAKAKAWAGLEGLDLAKDASTTQTFTWDEGLWSW 189

Query: 178 TGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIF 237
             G     K D+  + VV  D+G KRNILR L   G R T+VPA TSAED+L  NPDG+ 
Sbjct: 190 PEGYA---KLDKPKYEVVVIDYGVKRNILRALAHVGARATVVPASTSAEDILARNPDGVM 246

Query: 238 LSNGPGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHP 296
           LSNGPGDPA    YA+  IQK + +  PVFGICLGHQ+LALA GAKTVKM+ GHHG NHP
Sbjct: 247 LSNGPGDPAATGQYAVPEIQKLVASGKPVFGICLGHQMLALALGAKTVKMEQGHHGANHP 306

Query: 297 VKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEA 356
           VKD+    V I + NHGF VD A+LPA ++ TH SLFDGT  GI    KP FS Q HPEA
Sbjct: 307 VKDLTTGKVEIVSMNHGFTVDTASLPAPVKETHVSLFDGTNAGIALDGKPVFSVQHHPEA 366

Query: 357 SPGPHDAAPLFDHFIELIE 375
           SPGP D+  LF+ F  L++
Sbjct: 367 SPGPTDSLYLFERFAGLMD 385


Lambda     K      H
   0.318    0.135    0.400 

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: 490
Number of extensions: 23
Number of successful extensions: 5
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: 382
Length of database: 388
Length adjustment: 30
Effective length of query: 352
Effective length of database: 358
Effective search space:   126016
Effective search space used:   126016
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: 50 (23.9 bits)

Align candidate CCNA_02925 CCNA_02925 (carbamoyl-phosphate synthase small chain)
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.11271.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-128  415.2   0.0   1.2e-128  415.1   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02925  CCNA_02925 carbamoyl-phosphate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02925  CCNA_02925 carbamoyl-phosphate synthase small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.1   0.0  1.2e-128  1.2e-128       2     360 ..      12     385 ..      11     386 .. 0.94

  Alignments for each domain:
  == domain 1  score: 415.1 bits;  conditional E-value: 1.2e-128
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk....k 70 
                                           +l+l+dG +++g + ga +++vGev+FnT+mtGYqEiltDpsY  qiv +t p++gn+gvn ed+e      +
  lcl|FitnessBrowser__Caulo:CCNA_02925  12 VLALADGAILQGVGCGAVGDAVGEVCFNTAMTGYQEILTDPSYMAQIVAFTFPHVGNVGVNGEDVEQItgvaE 84 
                                           699**************************************************************86544458 PP

                             TIGR01368  71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelve 140
                                             ++g + +++ +   n+ra  ++++++k +g+v+++gvDTRal++k+Re+g  ++vi+++         lv+
  lcl|FitnessBrowser__Caulo:CCNA_02925  85 TAARGALFRDVPTVQANWRADGDFDAWMKARGVVGLAGVDTRALTRKIRETGMPHGVIAHSPDGqfdLAALVA 157
                                           999********************************************************98766443667888 PP

                             TIGR01368 141 kakespkvkevnlvkevstkeayeleq......k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpa 205
                                           kak+ + +++++l+k++st+++ ++ +      +  ak ++ k++vvvid+GvK+nilr L+++g++ tvvpa
  lcl|FitnessBrowser__Caulo:CCNA_02925 158 KAKAWAGLEGLDLAKDASTTQTFTWDEglwswpEgyAKLDKPKYEVVVIDYGVKRNILRALAHVGARATVVPA 230
                                           888999999*****************97776651668888889****************************** PP

                             TIGR01368 206 dtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGa 277
                                           +tsae+i + npdg++lsnGPGdPaa  ++a+ +++kl+ + +P+fGIclGhq+lalalgakt+k++ Gh+Ga
  lcl|FitnessBrowser__Caulo:CCNA_02925 231 STSAEDILARNPDGVMLSNGPGDPAATgQYAVPEIQKLVASGKPVFGICLGHQMLALALGAKTVKMEQGHHGA 303
                                           ************************776377899**************************************** PP

                             TIGR01368 278 NhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdtey 350
                                           Nhpvkdl+tg+vei s NHg++vd++sl++  ++ thv+l+Dgt++g++   +pvfsvQ+HPeaspGp+d+ y
  lcl|FitnessBrowser__Caulo:CCNA_02925 304 NHPVKDLTTGKVEIVSMNHGFTVDTASLPA-PVKETHVSLFDGTNAGIALDGKPVFSVQHHPEASPGPTDSLY 375
                                           ***************************885.5***************************************** PP

                             TIGR01368 351 lFdefvelik 360
                                           lF++f  l++
  lcl|FitnessBrowser__Caulo:CCNA_02925 376 LFERFAGLMD 385
                                           *****98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (388 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: 7.87
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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