Alignments for a candidate for carA in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Desulfurobacterium atlanticum DSM 15668

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_089322225.1 CHB58_RS00970 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_900188395.1:WP_089322225.1
          Length = 379

 Score =  367 bits (943), Expect = e-106
 Identities = 190/378 (50%), Positives = 246/378 (65%), Gaps = 7/378 (1%)

Query: 3   KSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGN 62
           K ALL LEDGT F G + GA G   GEVVF TSMTGYQEI+TDPS+  QIVT+T P IGN
Sbjct: 5   KKALLALEDGTVFEGVSFGAEGEVFGEVVFTTSMTGYQEIVTDPSFKGQIVTMTCPLIGN 64

Query: 63  VGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLL 122
           VG N  D ES +  A+G +++++  I SN+R       YL +H +V I++IDTR L + L
Sbjct: 65  VGANSEDVESERPQAEGFIVKEISEIYSNWRAEFSFEEYLSKHGVVGISEIDTRALVKKL 124

Query: 123 REKGAQNGCIIAGD-NPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGL 181
           R+ G   G I   D NP++ +  EKA + P + G++L  +V+  E Y W +G+W L  G 
Sbjct: 125 RDAGTMRGVISTVDLNPESLV--EKALSGPKMEGLNLVDKVSCKEPYEWNKGTWVLGKGY 182

Query: 182 PEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNG 241
            E     +  + V   DFG ++NILR LVD G +  ++PA+T  E++LK NPDG+FLS G
Sbjct: 183 LE---RSDFKYSVAVLDFGIRKNILRNLVDAGIKPVVLPAKTPPEEILKYNPDGVFLSCG 239

Query: 242 PGDPAPCDYAITAIQKFLET-DIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           PGDPA  DYAI  I+  + T + P+FGICLGHQL ALA G KT K+KFGH G N PV + 
Sbjct: 240 PGDPAAVDYAIETIKYLIATFNKPIFGICLGHQLTALALGGKTYKLKFGHRGANQPVLNK 299

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           +   V ITAQNHGFAV E T+P  L +TH SL D T++G+    KP F+ Q HPE+SPGP
Sbjct: 300 KTGKVEITAQNHGFAVSEETIPDELEITHISLNDKTVEGLKHKTKPIFTVQYHPESSPGP 359

Query: 361 HDAAPLFDHFIELIEQYR 378
           HD+  LF  F +LI  YR
Sbjct: 360 HDSRYLFREFAKLIADYR 377


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: 405
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: 379
Length adjustment: 30
Effective length of query: 352
Effective length of database: 349
Effective search space:   122848
Effective search space used:   122848
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_089322225.1 CHB58_RS00970 (glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit)
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.1070939.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-159  514.9   0.0   6.1e-159  514.7   0.0    1.0  1  NCBI__GCF_900188395.1:WP_089322225.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188395.1:WP_089322225.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.7   0.0  6.1e-159  6.1e-159       1     360 [.       7     374 ..       7     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 514.7 bits;  conditional E-value: 6.1e-159
                             TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikv 73 
                                           a l+ledGtvfeg sfgae+ev+GevvF+TsmtGYqEi+tDps+kgqiv++t plign+g n+ed+es+++++
  NCBI__GCF_900188395.1:WP_089322225.1   7 ALLALEDGTVFEGVSFGAEGEVFGEVVFTTSMTGYQEIVTDPSFKGQIVTMTCPLIGNVGANSEDVESERPQA 79 
                                           579********************************************************************** PP

                             TIGR01368  74 kglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakesp 146
                                           +g++vke+s+ +sn+ra+ s+ee+l+++g+v+i ++DTRalvkklR++g+m++vist + + e+lveka + p
  NCBI__GCF_900188395.1:WP_089322225.1  80 EGFIVKEISEIYSNWRAEFSFEEYLSKHGVVGISEIDTRALVKKLRDAGTMRGVISTVDLNPESLVEKALSGP 152
                                           ************************************************************************* PP

                             TIGR01368 147 kvkevnlvkevstkeayeleq......k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaee 211
                                           k++++nlv++vs+ke+ye+++      k   ++++ k++v+v+d+G+++nilr+Lv+ g++ +v+pa+t+ ee
  NCBI__GCF_900188395.1:WP_089322225.1 153 KMEGLNLVDKVSCKEPYEWNKgtwvlgKgyLERSDFKYSVAVLDFGIRKNILRNLVDAGIKPVVLPAKTPPEE 225
                                           ********************976666526678888889*********************************** PP

                             TIGR01368 212 ikklnpdgillsnGPGdPaaveeaietvkkllea.kiPifGIclGhqllalalgaktyklkfGhrGaNhpvkd 283
                                           i k+npdg++ls GPGdPaav++aiet+k l+ + ++PifGIclGhql+alalg+ktyklkfGhrGaN+pv +
  NCBI__GCF_900188395.1:WP_089322225.1 226 ILKYNPDGVFLSCGPGDPAAVDYAIETIKYLIATfNKPIFGICLGHQLTALALGGKTYKLKFGHRGANQPVLN 298
                                           ********************************999************************************** PP

                             TIGR01368 284 lktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefv 356
                                            ktg+veit+qNHg+av+ee+++ +ele+th +lnD+tvegl+hk++p+f+vQyHPe+spGphd++ylF+ef 
  NCBI__GCF_900188395.1:WP_089322225.1 299 KKTGKVEITAQNHGFAVSEETIP-DELEITHISLNDKTVEGLKHKTKPIFTVQYHPESSPGPHDSRYLFREFA 370
                                           *********************98.66*********************************************** PP

                             TIGR01368 357 elik 360
                                           +li+
  NCBI__GCF_900188395.1:WP_089322225.1 371 KLIA 374
                                           9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (379 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.65
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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