Alignments for a candidate for carA in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Novosphingobium aromaticivorans DSM 12444

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_011445875.1 SARO_RS11225 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000013325.1:WP_011445875.1
          Length = 391

 Score =  348 bits (894), Expect = e-100
 Identities = 195/375 (52%), Positives = 241/375 (64%), Gaps = 10/375 (2%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           + +LVL DG+   GR  GA G+AVGEV FNT+MTGYQE++TDPSY+ Q+VT T+PHIGNV
Sbjct: 16  TGVLVLADGSVAWGRGFGAAGAAVGEVCFNTAMTGYQEVMTDPSYAGQVVTFTFPHIGNV 75

Query: 64  GTNDADEESSQVH-AQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLL 122
           GTN  D ES     A G V+R+     +NFR       ++++   + I+ +DTR LTR +
Sbjct: 76  GTNPDDMESHDTPGAVGCVVREDVTAPANFRAAGTFQQWMEQQGKIGISGLDTRALTRRI 135

Query: 123 REKGAQNGCIIAGDNP---DAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTG 179
           R  GA N  +IA D     D    +E+AR++PGL GMDLA+ VT     +W    W L  
Sbjct: 136 RLSGAPNA-VIAHDPKGQFDIPALIERARSWPGLEGMDLARVVTRDGQEAWEGSVWHLGE 194

Query: 180 GLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLS 239
           G    K +     HVVA DFGAK NI R LV  G  +TIVPA+TS E +L + P G+FLS
Sbjct: 195 GF--TKPQGTGRPHVVAMDFGAKDNIFRNLVKAGADVTIVPAETSLETILSLKPAGVFLS 252

Query: 240 NGPGDPAPCD-YAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK 298
           NGPGDPA    YA+  IQK LE D+PVFGICLGHQ+LALA+GA+T KM  GH G NHPVK
Sbjct: 253 NGPGDPAATGAYAVPVIQKLLEMDMPVFGICLGHQMLALAAGARTTKMHQGHRGANHPVK 312

Query: 299 DVEKNVVMITAQNHGFAVDEA--TLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEA 356
            +E  VV IT+ NHGFAVD A   L   +  TH SLFDG+  GI    K AF  Q HPEA
Sbjct: 313 RIEDGVVEITSMNHGFAVDNAPGALGDKVIETHVSLFDGSNCGIAVKGKKAFGVQYHPEA 372

Query: 357 SPGPHDAAPLFDHFI 371
           SPGP D+  LF+ F+
Sbjct: 373 SPGPQDSFYLFEKFV 387


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: 477
Number of extensions: 23
Number of successful extensions: 6
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: 391
Length adjustment: 30
Effective length of query: 352
Effective length of database: 361
Effective search space:   127072
Effective search space used:   127072
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_011445875.1 SARO_RS11225 (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.1405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.3e-128  412.1   0.0   1.1e-127  411.9   0.0    1.0  1  lcl|NCBI__GCF_000013325.1:WP_011445875.1  SARO_RS11225 carbamoyl-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013325.1:WP_011445875.1  SARO_RS11225 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.9   0.0  1.1e-127  1.1e-127       2     358 ..      18     389 ..      17     391 .] 0.93

  Alignments for each domain:
  == domain 1  score: 411.9 bits;  conditional E-value: 1.1e-127
                                 TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk. 69 
                                               +lvl+dG+v  g++fga + +vGev+FnT+mtGYqE++tDpsY+gq+v++t p+ign+g+n++d+es+ 
  lcl|NCBI__GCF_000013325.1:WP_011445875.1  18 VLVLADGSVAWGRGFGAAGAAVGEVCFNTAMTGYQEVMTDPSYAGQVVTFTFPHIGNVGTNPDDMESHd 86 
                                               69*****************************************************************96 PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...k 135
                                               ++ + g vv+e  +++ n+ra  +++++++++g ++i g+DTRal++++R +g+ +avi+++ +     
  lcl|NCBI__GCF_000013325.1:WP_011445875.1  87 TPGAVGCVVREDVTAPANFRAAGTFQQWMEQQGKIGISGLDTRALTRRIRLSGAPNAVIAHDPKGqfdI 155
                                               899*********************************************************998764446 PP

                                 TIGR01368 136 eelvekakespkvkevnlvkevstkeayeleq......k..akkegkk.lrvvvidlGvKenilreLvk 195
                                                 l+e+a++ p +++++l++ v+ + + ++e       +  +k +g+   +vv++d+G K ni r+Lvk
  lcl|NCBI__GCF_000013325.1:WP_011445875.1 156 PALIERARSWPGLEGMDLARVVTRDGQEAWEGsvwhlgEgfTKPQGTGrPHVVAMDFGAKDNIFRNLVK 224
                                               78899999***********99999999999986665551664444443479****************** PP

                                 TIGR01368 196 rgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalal 263
                                                g++vt+vpa+ts+e+i +l+p g++lsnGPGdPaa   +a+  ++klle ++P+fGIclGhq+lala+
  lcl|NCBI__GCF_000013325.1:WP_011445875.1 225 AGADVTIVPAETSLETILSLKPAGVFLSNGPGDPAATgAYAVPVIQKLLEMDMPVFGICLGHQMLALAA 293
                                               **********************************8772678999************************* PP

                                 TIGR01368 264 gaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdees.lkeeelevthvnlnDgtveglehkelp 331
                                               ga+t k++ GhrGaNhpvk +++g veits NHg+avd++     +++  thv+l+Dg++ g++ k ++
  lcl|NCBI__GCF_000013325.1:WP_011445875.1 294 GARTTKMHQGHRGANHPVKRIEDGVVEITSMNHGFAVDNAPgALGDKVIETHVSLFDGSNCGIAVKGKK 362
                                               **************************************985456789********************** PP

                                 TIGR01368 332 vfsvQyHPeaspGphdteylFdefvel 358
                                               +f vQyHPeaspGp+d+ ylF++fv  
  lcl|NCBI__GCF_000013325.1:WP_011445875.1 363 AFGVQYHPEASPGPQDSFYLFEKFVAS 389
                                               ************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (391 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: 00:00:00.01
# Mc/sec: 9.58
//
[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