Alignments for a candidate for carA in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Prosthecochloris aestuarii DSM 271

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_012506650.1 PAES_RS10520 carbamoyl-phosphate synthase small chain

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000020625.1:WP_012506650.1
          Length = 371

 Score =  365 bits (938), Expect = e-106
 Identities = 186/380 (48%), Positives = 255/380 (67%), Gaps = 21/380 (5%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           A LVLE+G+ + G A G  G   GEVVFNT++TGYQEI+TDPSY+ Q+V +TYP IGN G
Sbjct: 6   AKLVLENGSVYTGYAFGHIGETGGEVVFNTALTGYQEIVTDPSYAGQMVVMTYPLIGNYG 65

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            N +D ES ++ A  L++R++  I SNF  T  L  YLK   ++ +A IDTRKL R +R+
Sbjct: 66  VNQSDAESQKIWASALIVREMSNIHSNFAATGSLDQYLKEAKVMGLAGIDTRKLVREIRQ 125

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGA  G I A D PD     EKA   P + G+DL K+V+T++ Y+               
Sbjct: 126 KGAMRGVISAID-PDEKRLEEKALKIPEMTGLDLVKKVSTSQTYTIDC------------ 172

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
              D+  +HVVAYD+G K+NILRML +  C++T++ A T  E+ LK++PDGIFLSNGPGD
Sbjct: 173 ---DDAEYHVVAYDYGIKQNILRMLQNAKCKVTVLNANTPIEEALKLDPDGIFLSNGPGD 229

Query: 245 PAPCDYAITAIQKFLETD-----IPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKD 299
           P    YAI  I+K  E +     +P+FGICLGHQL++LA GAKT K+KFGHHG NHPVK+
Sbjct: 230 PFAVTYAIDNIKKLAEHNTQQKPVPLFGICLGHQLMSLAFGAKTYKLKFGHHGSNHPVKN 289

Query: 300 VEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPG 359
           ++ + + IT+QNHGFAV   +LP +L +TH +L+D T++G+     P FS Q HPEA+PG
Sbjct: 290 LKSSSIEITSQNHGFAVAMESLPESLEMTHLNLYDQTVEGVRHKKLPCFSVQYHPEAAPG 349

Query: 360 PHDAAPLFDHFIELIEQYRK 379
           PHD+  LF+ F  +++Q ++
Sbjct: 350 PHDSHYLFEQFTAMMDQAKE 369


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: 398
Number of extensions: 18
Number of successful extensions: 4
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: 371
Length adjustment: 30
Effective length of query: 352
Effective length of database: 341
Effective search space:   120032
Effective search space used:   120032
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 WP_012506650.1 PAES_RS10520 (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.8944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-155  502.3   0.3   4.1e-155  502.1   0.3    1.0  1  lcl|NCBI__GCF_000020625.1:WP_012506650.1  PAES_RS10520 carbamoyl-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020625.1:WP_012506650.1  PAES_RS10520 carbamoyl-phosphate synthase small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.1   0.3  4.1e-155  4.1e-155       1     360 [.       6     365 ..       6     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 502.1 bits;  conditional E-value: 4.1e-155
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a+lvle+G+v++g++fg+ +e+ GevvFnT++tGYqEi+tDpsY+gq+vv+typlignygvn++daes+
  lcl|NCBI__GCF_000020625.1:WP_012506650.1   6 AKLVLENGSVYTGYAFGHIGETGGEVVFNTALTGYQEIVTDPSYAGQMVVMTYPLIGNYGVNQSDAESQ 74 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138
                                               ki++++l+v+e+s+  sn+ a+ sL+++lke ++++++g+DTR+lv+++R+kg+m++vis+ + ++++l
  lcl|NCBI__GCF_000020625.1:WP_012506650.1  75 KIWASALIVREMSNIHSNFAATGSLDQYLKEAKVMGLAGIDTRKLVREIRQKGAMRGVISAIDPDEKRL 143
                                               ********************************************************************* PP

                                 TIGR01368 139 vekakespkvkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadt 207
                                               +eka + p++++++lvk+vst+++y++      ++ +++vv++d+G+K+nilr+L++ +++vtv++a+t
  lcl|NCBI__GCF_000020625.1:WP_012506650.1 144 EEKALKIPEMTGLDLVKKVSTSQTYTIDC----DDAEYHVVAYDYGIKQNILRMLQNAKCKVTVLNANT 208
                                               *************************9995....677789****************************** PP

                                 TIGR01368 208 saeeikklnpdgillsnGPGdPaaveeaietvkkllea.....kiPifGIclGhqllalalgaktyklk 271
                                               ++ee  kl+pdgi+lsnGPGdP av++ai+++kkl+e+      +P+fGIclGhql++la+gaktyklk
  lcl|NCBI__GCF_000020625.1:WP_012506650.1 209 PIEEALKLDPDGIFLSNGPGDPFAVTYAIDNIKKLAEHntqqkPVPLFGICLGHQLMSLAFGAKTYKLK 277
                                               ***********************************99766655689*********************** PP

                                 TIGR01368 272 fGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPe 340
                                               fGh+G+Nhpvk+lk+  +eitsqNHg+av  esl+ e+le+th nl+D+tveg++hk+lp+fsvQyHPe
  lcl|NCBI__GCF_000020625.1:WP_012506650.1 278 FGHHGSNHPVKNLKSSSIEITSQNHGFAVAMESLP-ESLEMTHLNLYDQTVEGVRHKKLPCFSVQYHPE 345
                                               *********************************88.56******************************* PP

                                 TIGR01368 341 aspGphdteylFdefvelik 360
                                               a+pGphd++ylF++f+ +++
  lcl|NCBI__GCF_000020625.1:WP_012506650.1 346 AAPGPHDSHYLFEQFTAMMD 365
                                               ****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (371 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.61
//
[ok]

This GapMind analysis is from Apr 10 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis