Alignments for a candidate for carA in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Thiohalomonas denitrificans HLD2

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_092992287.1 BLP65_RS00865 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_900102855.1:WP_092992287.1
          Length = 381

 Score =  555 bits (1430), Expect = e-163
 Identities = 267/379 (70%), Positives = 313/379 (82%), Gaps = 3/379 (0%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           M + ALL LEDGT F G +IG  G  VGEVVFNT+MTGYQEILTDPSY +QIVTLTYPHI
Sbjct: 1   MRQPALLALEDGTLFWGESIGIEGQTVGEVVFNTAMTGYQEILTDPSYYKQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GNVGTN  DEES+ V A GLVIRDLPL+ SN+R+   L  YL+++++V IADIDTR+LTR
Sbjct: 61  GNVGTNAEDEESAHVFASGLVIRDLPLLTSNWRSEMPLDKYLQKNSVVGIADIDTRRLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LREKGAQNGCI+AG++ DA  AL  AR FPGL GMDLAKEV+T + Y W Q SW L  G
Sbjct: 121 VLREKGAQNGCIMAGEHIDANTALAAARGFPGLKGMDLAKEVSTHQPYEWAQASWDLESG 180

Query: 181 LP---EAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIF 237
           LP   E   E+ LP+HVV +D+G KRNILRMLVDRGCR+T+VPA+T  E V+++ PDG+F
Sbjct: 181 LPGHPEGPIEEALPYHVVTWDYGIKRNILRMLVDRGCRVTVVPAETPVEKVMELKPDGVF 240

Query: 238 LSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPV 297
           LSNGPGDP PCDYAI AIQK L+  IP +GICLGHQLLALASGAKT KMKFGHHG NHPV
Sbjct: 241 LSNGPGDPEPCDYAIRAIQKVLDAGIPTYGICLGHQLLALASGAKTEKMKFGHHGANHPV 300

Query: 298 KDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEAS 357
           +D+E   VMIT+QNHGF+VDE++LPANL+ TH+SLFDG+LQGIHRTD PAFSFQGHPEAS
Sbjct: 301 QDLETKKVMITSQNHGFSVDESSLPANLKATHRSLFDGSLQGIHRTDCPAFSFQGHPEAS 360

Query: 358 PGPHDAAPLFDHFIELIEQ 376
           PGP D APLFDHFI+L+++
Sbjct: 361 PGPRDVAPLFDHFIDLMKE 379


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: 515
Number of extensions: 15
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: 381
Length adjustment: 30
Effective length of query: 352
Effective length of database: 351
Effective search space:   123552
Effective search space used:   123552
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_092992287.1 BLP65_RS00865 (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.1066505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-148  478.9   0.0   5.4e-148  478.7   0.0    1.0  1  NCBI__GCF_900102855.1:WP_092992287.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900102855.1:WP_092992287.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.7   0.0  5.4e-148  5.4e-148       1     360 [.       5     378 ..       5     379 .. 0.95

  Alignments for each domain:
  == domain 1  score: 478.7 bits;  conditional E-value: 5.4e-148
                             TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikv 73 
                                           a l+ledGt f g+s+g e+++vGevvFnT+mtGYqEiltDpsY +qiv+ltyp+ign+g+n+ed+es ++ +
  NCBI__GCF_900102855.1:WP_092992287.1   5 ALLALEDGTLFWGESIGIEGQTVGEVVFNTAMTGYQEILTDPSYYKQIVTLTYPHIGNVGTNAEDEESAHVFA 77 
                                           579********************************************************************** PP

                             TIGR01368  74 kglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek.sekeelvekakes 145
                                           +glv+++l   +sn+r++  L+++l+++ +v+i+++DTR l++ lRekg+++++i++ + ++++++ ++a+  
  NCBI__GCF_900102855.1:WP_092992287.1  78 SGLVIRDLPLLTSNWRSEMPLDKYLQKNSVVGIADIDTRRLTRVLREKGAQNGCIMAGEhIDANTALAAARGF 150
                                           ******************************************************998761557788899999* PP

                             TIGR01368 146 pkvkevnlvkevstkeayeleq...........k...akkegkk.lrvvvidlGvKenilreLvkrgvevtvv 203
                                           p +k+++l+kevst+++ye+ q           +     +e    ++vv  d+G+K+nilr+Lv+rg++vtvv
  NCBI__GCF_900102855.1:WP_092992287.1 151 PGLKGMDLAKEVSTHQPYEWAQaswdlesglpgHpegPIEEA-LpYHVVTWDYGIKRNILRMLVDRGCRVTVV 222
                                           *********************988877666555154423333.3479************************** PP

                             TIGR01368 204 padtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrG 276
                                           pa+t++e++++l+pdg++lsnGPGdP+ +++ai+ ++k+l+a iP++GIclGhqllala+gakt k+kfGh+G
  NCBI__GCF_900102855.1:WP_092992287.1 223 PAETPVEKVMELKPDGVFLSNGPGDPEPCDYAIRAIQKVLDAGIPTYGICLGHQLLALASGAKTEKMKFGHHG 295
                                           ************************************************************************* PP

                             TIGR01368 277 aNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdte 349
                                           aNhpv+dl+t++v+itsqNHg++vde+sl+++ l++th++l+Dg+++g+++++ p+fs Q HPeaspGp+d +
  NCBI__GCF_900102855.1:WP_092992287.1 296 ANHPVQDLETKKVMITSQNHGFSVDESSLPAN-LKATHRSLFDGSLQGIHRTDCPAFSFQGHPEASPGPRDVA 367
                                           ****************************8866.**************************************** PP

                             TIGR01368 350 ylFdefvelik 360
                                            lFd+f++l+k
  NCBI__GCF_900102855.1:WP_092992287.1 368 PLFDHFIDLMK 378
                                           *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (381 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 14.29
//
[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