GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Pseudomonas putida KT2440

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate PP_4724 PP_4724 Carbamoyl-phosphate synthase small chain

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Putida:PP_4724
          Length = 378

 Score =  539 bits (1389), Expect = e-158
 Identities = 264/378 (69%), Positives = 301/378 (79%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           M K A+L L DG+ F G AIGA G  VGEVVFNT+MTGYQEILTDPSY++QIVTLTYPHI
Sbjct: 1   MTKPAILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GN GT   D ESS+V + GLVIRDLPL+ASN+RNT+ L  YLK +N+VAIA IDTR+LTR
Sbjct: 61  GNTGTTPEDAESSRVWSAGLVIRDLPLLASNWRNTQSLPEYLKANNVVAIAGIDTRRLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LREKGAQNGCI+AGDN     A+  AR FPGL GMDLAK V+T E Y W    W L   
Sbjct: 121 ILREKGAQNGCILAGDNISEEAAIAAARGFPGLKGMDLAKVVSTKERYEWRSSVWELKTD 180

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
                   +LP+HVVA+D+G K NILRMLV RGCR+T+VPAQT A +VL +NPDG+FLSN
Sbjct: 181 SHPTIDAADLPYHVVAFDYGVKLNILRMLVARGCRVTVVPAQTPASEVLALNPDGVFLSN 240

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDP PCDYAI AI++ LET+IPVFGICLGHQLLALASGAKTVKM  GHHG NHPV+D+
Sbjct: 241 GPGDPEPCDYAIQAIKEILETEIPVFGICLGHQLLALASGAKTVKMGHGHHGANHPVQDL 300

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           +  VVMIT+QNHGFAVDEATLP N+R  HKSLFDGTLQGI RTDK AFSFQGHPEASPGP
Sbjct: 301 DTGVVMITSQNHGFAVDEATLPGNVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGP 360

Query: 361 HDAAPLFDHFIELIEQYR 378
            D APLFD F + + + R
Sbjct: 361 TDVAPLFDRFTDAMAKRR 378


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: 514
Number of extensions: 10
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: 382
Length of database: 378
Length adjustment: 30
Effective length of query: 352
Effective length of database: 348
Effective search space:   122496
Effective search space used:   122496
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 PP_4724 PP_4724 (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.31651.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.6e-147  474.7   0.0   9.8e-147  474.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4724  PP_4724 Carbamoyl-phosphate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4724  PP_4724 Carbamoyl-phosphate synthase small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.5   0.0  9.8e-147  9.8e-147       1     360 [.       5     375 ..       5     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 474.5 bits;  conditional E-value: 9.8e-147
                           TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkg 75 
                                         a+l+l+dG++f+g+++ga++++vGevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+g+++edaes++++ +g
  lcl|FitnessBrowser__Putida:PP_4724   5 AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHIGNTGTTPEDAESSRVWSAG 79 
                                         689************************************************************************ PP

                           TIGR01368  76 lvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvk 149
                                         lv+++l   +sn+r+++sL e+lk +++vai+g+DTR l++ lRekg+++++i + ++  +e ++++a+  p +k
  lcl|FitnessBrowser__Putida:PP_4724  80 LVIRDLPLLASNWRNTQSLPEYLKANNVVAIAGIDTRRLTRILREKGAQNGCILAGDNIsEEAAIAAARGFPGLK 154
                                         ****************************************************998775427778889999***** PP

                           TIGR01368 150 evnlvkevstkeayeleq.......k....akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeik 213
                                         +++l+k vstke+ye+++       +    + + +  ++vv++d+GvK nilr+Lv+rg++vtvvpa+t+a+e+ 
  lcl|FitnessBrowser__Putida:PP_4724 155 GMDLAKVVSTKERYEWRSsvwelktDshptIDAADLPYHVVAFDYGVKLNILRMLVARGCRVTVVPAQTPASEVL 229
                                         *****************977766551555455566669************************************* PP

                           TIGR01368 214 klnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgr 288
                                         +lnpdg++lsnGPGdP+ +++ai+ +k++le++iP+fGIclGhqllala+gakt+k+  Gh+GaNhpv+dl+tg 
  lcl|FitnessBrowser__Putida:PP_4724 230 ALNPDGVFLSNGPGDPEPCDYAIQAIKEILETEIPVFGICLGHQLLALASGAKTVKMGHGHHGANHPVQDLDTGV 304
                                         *************************************************************************** PP

                           TIGR01368 289 veitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                         v+itsqNHg+avde++l+ +++++ h++l+Dgt++g+e++++ +fs Q HPeaspGp+d + lFd+f+++++
  lcl|FitnessBrowser__Putida:PP_4724 305 VMITSQNHGFAVDEATLP-GNVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGPTDVAPLFDRFTDAMA 375
                                         ***************977.66***********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (378 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: 7.56
//
[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