GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Marinobacter adhaerens HP15

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate GFF3136 HP15_3078 carbamoyl-phosphate synthase small chain

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Marino:GFF3136
          Length = 376

 Score =  536 bits (1381), Expect = e-157
 Identities = 261/375 (69%), Positives = 304/375 (81%), Gaps = 3/375 (0%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           M   A+L L DG+ F+G AIGA G   GEVVFNT+MTGYQEILTDPSYSRQIVTLTYPHI
Sbjct: 1   MSTPAILALADGSLFYGTAIGADGETSGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GN G N+ D ES ++ A GL+IRDLPL+AS++R+   L  YL+ +NIV IADIDTR+LTR
Sbjct: 61  GNTGVNEEDVESDRIQAAGLIIRDLPLLASSWRSKGTLDDYLRSNNIVGIADIDTRRLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LR+KG+QNG I+AG+N  A  ALE A+AFPGL GMDLAKEVT+ + +SW +  WTL  G
Sbjct: 121 ILRDKGSQNGAIVAGENATAERALELAKAFPGLKGMDLAKEVTSDKTWSWKETEWTLEEG 180

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
             E    +E  F VVA+D+G K NILRML  RGC +T+VPAQT A +VL MNPDG+FLSN
Sbjct: 181 YGE---REESRFKVVAWDYGVKLNILRMLASRGCDITVVPAQTPASEVLAMNPDGVFLSN 237

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDP PCDYAITAI++ LET+IPVFGICLGHQLLALASGAKT+KM  GHHG NHPV+++
Sbjct: 238 GPGDPEPCDYAITAIKEVLETEIPVFGICLGHQLLALASGAKTMKMGHGHHGANHPVQEI 297

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
               VMIT+QNHGFAVDEATLPAN+  THKSLFDGTLQGI RTDKPA+SFQGHPEASPGP
Sbjct: 298 ATGTVMITSQNHGFAVDEATLPANVEATHKSLFDGTLQGIRRTDKPAYSFQGHPEASPGP 357

Query: 361 HDAAPLFDHFIELIE 375
           HD APLFD FI L+E
Sbjct: 358 HDVAPLFDEFIRLME 372


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: 519
Number of extensions: 9
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: 376
Length adjustment: 30
Effective length of query: 352
Effective length of database: 346
Effective search space:   121792
Effective search space used:   121792
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 GFF3136 HP15_3078 (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.17449.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-149  483.9   0.0   1.6e-149  483.7   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3136  HP15_3078 carbamoyl-phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3136  HP15_3078 carbamoyl-phosphate synthase small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.7   0.0  1.6e-149  1.6e-149       1     360 [.       5     372 ..       5     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 483.7 bits;  conditional E-value: 1.6e-149
                           TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkg 75 
                                         a+l+l+dG+ f g+++ga++e+ GevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+gvneed+es++i+++g
  lcl|FitnessBrowser__Marino:GFF3136   5 AILALADGSLFYGTAIGADGETSGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHIGNTGVNEEDVESDRIQAAG 79 
                                         689************************************************************************ PP

                           TIGR01368  76 lvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvk 149
                                         l++++l   +s++r+k +L+++l++++iv+i+++DTR l++ lR+kgs++++i++ +++ +e++ e ak+ p +k
  lcl|FitnessBrowser__Marino:GFF3136  80 LIIRDLPLLASSWRSKGTLDDYLRSNNIVGIADIDTRRLTRILRDKGSQNGAIVAGENAtAERALELAKAFPGLK 154
                                         ***************************************************99987765378889999******* PP

                           TIGR01368 150 evnlvkevstkeayeleq.....k...akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikkln 216
                                         +++l+kev+ +++ ++++     +    ++e+++ +vv+ d+GvK nilr+L++rg+++tvvpa+t+a+e+ ++n
  lcl|FitnessBrowser__Marino:GFF3136 155 GMDLAKEVTSDKTWSWKEtewtlEegyGEREESRFKVVAWDYGVKLNILRMLASRGCDITVVPAQTPASEVLAMN 229
                                         *****************966655156667888889**************************************** PP

                           TIGR01368 217 pdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrvei 291
                                         pdg++lsnGPGdP+ +++ai+ +k++le++iP+fGIclGhqllala+gakt+k+  Gh+GaNhpv++++tg+v+i
  lcl|FitnessBrowser__Marino:GFF3136 230 PDGVFLSNGPGDPEPCDYAITAIKEVLETEIPVFGICLGHQLLALASGAKTMKMGHGHHGANHPVQEIATGTVMI 304
                                         *************************************************************************** PP

                           TIGR01368 292 tsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                         tsqNHg+avde++l+++ +e+th++l+Dgt++g++++++p++s Q HPeaspGphd + lFdef++l++
  lcl|FitnessBrowser__Marino:GFF3136 305 TSQNHGFAVDEATLPAN-VEATHKSLFDGTLQGIRRTDKPAYSFQGHPEASPGPHDVAPLFDEFIRLME 372
                                         *************8866.************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (376 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: 00:00:00.01
# Mc/sec: 8.92
//
[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