Alignments for a candidate for carA in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Thermithiobacillus tepidarius DSM 3134

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_038018886.1 G579_RS0107820 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000423825.1:WP_038018886.1
          Length = 385

 Score =  522 bits (1344), Expect = e-153
 Identities = 254/380 (66%), Positives = 303/380 (79%), Gaps = 2/380 (0%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           ALL LEDGT F G  IG+ G AVGE+ FNT+MTGYQEILTDPSY+RQIVTLTYPHIGNVG
Sbjct: 3   ALLALEDGTLFWGEGIGSQGQAVGELCFNTAMTGYQEILTDPSYARQIVTLTYPHIGNVG 62

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
           TN AD ES  V+A GLVIRDLP  ASN+R+ + L  YLK + +VAIA IDTR+LTRLLRE
Sbjct: 63  TNRADAESGAVYAAGLVIRDLPRRASNWRSEQTLERYLKDNRVVAIAGIDTRQLTRLLRE 122

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGAQN  ++ G++ DA  AL  AR FPGL+GMDLAK V+    Y W QGSWTL GGLP A
Sbjct: 123 KGAQNAALVCGEHIDAEAALAAARNFPGLDGMDLAKVVSEPAPYEWAQGSWTLAGGLPHA 182

Query: 185 KK--EDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGP 242
               +++LP HVVAYDFG KRNILRMLVDRGCR+T+VPA+T A +VL ++PDG+FLSNGP
Sbjct: 183 PHPLDEKLPRHVVAYDFGIKRNILRMLVDRGCRVTVVPAETPAREVLALDPDGVFLSNGP 242

Query: 243 GDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEK 302
           GDPAP DYA  A ++ LE  +P++GICLGHQLL LA GAK++KMKFGHHG NHPVKD++ 
Sbjct: 243 GDPAPMDYAQQATREILEQGVPLYGICLGHQLLCLALGAKSLKMKFGHHGANHPVKDLDS 302

Query: 303 NVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHD 362
             V I++QNHGFA+D  TLPA LRV+H SLFDG+LQG+  T+ PAFSFQGHPEASPGPH+
Sbjct: 303 GRVFISSQNHGFAIDAETLPATLRVSHVSLFDGSLQGVAHTELPAFSFQGHPEASPGPHE 362

Query: 363 AAPLFDHFIELIEQYRKTAK 382
              LFD F++ I+ YRK+ +
Sbjct: 363 MGYLFDRFVDQIDAYRKSRR 382


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: 527
Number of extensions: 14
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: 385
Length adjustment: 30
Effective length of query: 352
Effective length of database: 355
Effective search space:   124960
Effective search space used:   124960
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_038018886.1 G579_RS0107820 (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.14831.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-144  467.2   0.0   1.9e-144  467.0   0.0    1.0  1  lcl|NCBI__GCF_000423825.1:WP_038018886.1  G579_RS0107820 carbamoyl-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000423825.1:WP_038018886.1  G579_RS0107820 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.0   0.0  1.9e-144  1.9e-144       1     360 [.       3     375 ..       3     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 467.0 bits;  conditional E-value: 1.9e-144
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a l+ledGt f g+++g+++++vGe++FnT+mtGYqEiltDpsY++qiv+ltyp+ign+g+n+ daes 
  lcl|NCBI__GCF_000423825.1:WP_038018886.1   3 ALLALEDGTLFWGEGIGSQGQAVGELCFNTAMTGYQEILTDPSYARQIVTLTYPHIGNVGTNRADAESG 71 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavist.eksekee 137
                                                ++++glv+++l +++sn+r++++Le++lk++ +vai+g+DTR+l++ lRekg+++a+++  e++++e 
  lcl|NCBI__GCF_000423825.1:WP_038018886.1  72 AVYAAGLVIRDLPRRASNWRSEQTLERYLKDNRVVAIAGIDTRQLTRLLREKGAQNAALVCgEHIDAEA 140
                                               *******************************************************99877615667889 PP

                                 TIGR01368 138 lvekakespkvkevnlvkevstkeayeleq..........k..akkegkk.lrvvvidlGvKenilreL 193
                                               + ++a++ p +++++l+k vs   +ye+ q          +  +  ++k  ++vv++d+G+K+nilr+L
  lcl|NCBI__GCF_000423825.1:WP_038018886.1 141 ALAAARNFPGLDGMDLAKVVSEPAPYEWAQgswtlagglpHapHPLDEKLpRHVVAYDFGIKRNILRML 209
                                               9999*************************988877766651554445555689**************** PP

                                 TIGR01368 194 vkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllala 262
                                               v+rg++vtvvpa+t+a+e+ +l+pdg++lsnGPGdPa +++a + ++++le+ +P++GIclGhqll+la
  lcl|NCBI__GCF_000423825.1:WP_038018886.1 210 VDRGCRVTVVPAETPAREVLALDPDGVFLSNGPGDPAPMDYAQQATREILEQGVPLYGICLGHQLLCLA 278
                                               ********************************************************************* PP

                                 TIGR01368 263 lgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelp 331
                                               lgak +k+kfGh+GaNhpvkdl++grv+i+sqNHg+a+d e+l+++ l+v hv+l+Dg+++g++h+elp
  lcl|NCBI__GCF_000423825.1:WP_038018886.1 279 LGAKSLKMKFGHHGANHPVKDLDSGRVFISSQNHGFAIDAETLPAT-LRVSHVSLFDGSLQGVAHTELP 346
                                               ******************************************8866.********************** PP

                                 TIGR01368 332 vfsvQyHPeaspGphdteylFdefvelik 360
                                               +fs Q HPeaspGph+  ylFd+fv++i+
  lcl|NCBI__GCF_000423825.1:WP_038018886.1 347 AFSFQGHPEASPGPHEMGYLFDRFVDQID 375
                                               *************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (385 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: 00:00:00.02
# Mc/sec: 6.64
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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