Alignments for a candidate for carA in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Halomonas desiderata SP1

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_086510468.1 BZY95_RS13635 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_002151265.1:WP_086510468.1
          Length = 386

 Score =  529 bits (1362), Expect = e-155
 Identities = 259/380 (68%), Positives = 299/380 (78%), Gaps = 5/380 (1%)

Query: 3   KSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGN 62
           + A+L LEDG+ FHG AIGA G   GEVVFNT+MTGYQEILTD SY+RQIVTLTYPHIGN
Sbjct: 8   RPAILALEDGSVFHGTAIGADGQTSGEVVFNTAMTGYQEILTDLSYTRQIVTLTYPHIGN 67

Query: 63  VGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLL 122
            G N  D ES  + A GLVIRDLPLIASNFR+ + LS YLK  N++ IADIDTR+LTR+L
Sbjct: 68  TGVNAEDVESGSIAAAGLVIRDLPLIASNFRSEQSLSDYLKSQNVLGIADIDTRRLTRIL 127

Query: 123 REKGAQNGCIIAGDNPDAALALEKA----RAFPGLNGMDLAKEVTTAEAYSWTQGSWTLT 178
           R+KGAQNG I+AG   +   A+E+A    RAFPGL GMDLAKEV+  +AY W +  W L 
Sbjct: 128 RDKGAQNGAILAGREAEGEDAVERALAAARAFPGLKGMDLAKEVSCKQAYEWNEAEWVLG 187

Query: 179 GGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFL 238
            G  +A    E PFHVV YD+G K NILRML  RGCRLT+VPAQT A DVL  NPDGI L
Sbjct: 188 QGNVDASGS-ERPFHVVVYDYGVKYNILRMLASRGCRLTVVPAQTPASDVLARNPDGILL 246

Query: 239 SNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK 298
           +NGPGDPAPCDYAI AIQ+ LETD+PVFGICLGHQLLALA+GAKTVKM  GHHG NHPV+
Sbjct: 247 ANGPGDPAPCDYAIKAIQEILETDVPVFGICLGHQLLALAAGAKTVKMNHGHHGANHPVQ 306

Query: 299 DVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358
           D++   VMIT+QNHGFAVDEA+LP N+R  H+SLFDGTLQGI  TD+PAFSFQGHPEASP
Sbjct: 307 DLDSGHVMITSQNHGFAVDEASLPGNVRAIHRSLFDGTLQGIELTDRPAFSFQGHPEASP 366

Query: 359 GPHDAAPLFDHFIELIEQYR 378
           GP D +PLFD F+ ++ + R
Sbjct: 367 GPRDVSPLFDRFVTMMRERR 386


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: 540
Number of extensions: 13
Number of successful extensions: 3
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: 386
Length adjustment: 30
Effective length of query: 352
Effective length of database: 356
Effective search space:   125312
Effective search space used:   125312
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_086510468.1 BZY95_RS13635 (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.13671.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-146  473.1   0.0     3e-146  472.9   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510468.1  BZY95_RS13635 carbamoyl-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510468.1  BZY95_RS13635 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.9   0.0    3e-146    3e-146       1     360 [.      10     383 ..      10     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 472.9 bits;  conditional E-value: 3e-146
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a+l+ledG+vf+g+++ga++++ GevvFnT+mtGYqEiltD sY++qiv+ltyp+ign+gvn+ed+es 
  lcl|NCBI__GCF_002151265.1:WP_086510468.1  10 AILALEDGSVFHGTAIGADGQTSGEVVFNTAMTGYQEILTDLSYTRQIVTLTYPHIGNTGVNAEDVESG 78 
                                               689****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.... 134
                                               +i ++glv+++l   +sn+r+++sL+++lk++++ +i+++DTR l++ lR+kg+++++i + +++    
  lcl|NCBI__GCF_002151265.1:WP_086510468.1  79 SIAAAGLVIRDLPLIASNFRSEQSLSDYLKSQNVLGIADIDTRRLTRILRDKGAQNGAILAGREAeged 147
                                               ***********************************************************9887666666 PP

                                 TIGR01368 135 .keelvekakespkvkevnlvkevstkeayeleq......k....akkegkklrvvvidlGvKenilre 192
                                                 e++ ++a++ p +k+++l+kevs+k+aye+++      +    a+ +++  +vvv+d+GvK nilr+
  lcl|NCBI__GCF_002151265.1:WP_086510468.1 148 aVERALAAARAFPGLKGMDLAKEVSCKQAYEWNEaewvlgQgnvdASGSERPFHVVVYDYGVKYNILRM 216
                                               6778888899***********************97776661554345555559**************** PP

                                 TIGR01368 193 LvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllal 261
                                               L++rg+++tvvpa+t+a+++ + npdgill+nGPGdPa +++ai+ ++++le+++P+fGIclGhqllal
  lcl|NCBI__GCF_002151265.1:WP_086510468.1 217 LASRGCRLTVVPAQTPASDVLARNPDGILLANGPGDPAPCDYAIKAIQEILETDVPVFGICLGHQLLAL 285
                                               ********************************************************************* PP

                                 TIGR01368 262 algaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkel 330
                                               a+gakt+k++ Gh+GaNhpv+dl++g+v+itsqNHg+avde+sl+ +++++ h++l+Dgt++g+e ++ 
  lcl|NCBI__GCF_002151265.1:WP_086510468.1 286 AAGAKTVKMNHGHHGANHPVQDLDSGHVMITSQNHGFAVDEASLP-GNVRAIHRSLFDGTLQGIELTDR 353
                                               *******************************************87.66********************* PP

                                 TIGR01368 331 pvfsvQyHPeaspGphdteylFdefvelik 360
                                               p+fs Q HPeaspGp+d + lFd+fv++++
  lcl|NCBI__GCF_002151265.1:WP_086510468.1 354 PAFSFQGHPEASPGPRDVSPLFDRFVTMMR 383
                                               ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (386 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: 7.09
//
[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