Alignments for a candidate for carA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Dyella japonica UNC79MFTsu3.2

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate N515DRAFT_2714 N515DRAFT_2714 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2714
          Length = 375

 Score =  512 bits (1318), Expect = e-150
 Identities = 249/374 (66%), Positives = 299/374 (79%), Gaps = 3/374 (0%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           ALL LEDG+ FHG+A+GATG  VGEVVFNT+MTGYQEILTDPSYSRQIVTLTYPHIGN G
Sbjct: 5   ALLALEDGSVFHGQAVGATGETVGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHIGNTG 64

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            N  D ES  VHA GL++RD+P  ASN+R++E L  YLKR  IVAIA IDTR+LTR+LR+
Sbjct: 65  VNAEDAESLAVHAAGLIVRDVPRRASNWRSSESLPDYLKRLGIVAIAGIDTRRLTRILRD 124

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGA  GCI+AG++ DA  AL KARAFPGLNGMDLAK V+  + Y+W +GS+ L     +A
Sbjct: 125 KGALAGCIVAGEHVDAEAALAKARAFPGLNGMDLAKVVSVTKPYAWKEGSYDLDR---QA 181

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
            ++  L F VVAYD+G K NILR+L  +GC +T+VPAQT A +VL M PDG+FLSNGPGD
Sbjct: 182 FEQPALRFKVVAYDYGVKFNILRLLAAQGCDITVVPAQTPAAEVLAMKPDGVFLSNGPGD 241

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           PA CDYA+ A ++FL+  IP+FGICLGHQ++ LA GAKT+KMKFGHHG NHPVKD +   
Sbjct: 242 PAACDYAVAATREFLDAKIPLFGICLGHQIMGLALGAKTLKMKFGHHGANHPVKDHDDGR 301

Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364
           V+IT+QNHGFAVD ATLPAN+RVTH SLFDG+LQG   TD+PAF FQGHPEASPGPHD  
Sbjct: 302 VLITSQNHGFAVDPATLPANVRVTHSSLFDGSLQGFALTDRPAFCFQGHPEASPGPHDIG 361

Query: 365 PLFDHFIELIEQYR 378
            LF+ F +L+++ R
Sbjct: 362 YLFERFAQLMQESR 375


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: 502
Number of extensions: 13
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: 375
Length adjustment: 30
Effective length of query: 352
Effective length of database: 345
Effective search space:   121440
Effective search space used:   121440
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 N515DRAFT_2714 N515DRAFT_2714 (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.28510.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.8e-149  482.9   0.0   3.2e-149  482.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714  N515DRAFT_2714 carbamoyl-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2714  N515DRAFT_2714 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.7   0.0  3.2e-149  3.2e-149       1     360 [.       5     372 ..       5     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 482.7 bits;  conditional E-value: 3.2e-149
                                    TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneeda 66 
                                                  a l+ledG+vf+g+++ga++e+vGevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+gvn+eda
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714   5 ALLALEDGSVFHGQAVGATGETVGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHIGNTGVNAEDA 70 
                                                  579*************************************************************** PP

                                    TIGR01368  67 eskkikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek 132
                                                  es  ++++gl+v+++ +++sn+r++esL ++lk+ givai+g+DTR l++ lR+kg+++++i++ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714  71 ESLAVHAAGLIVRDVPRRASNWRSSESLPDYLKRLGIVAIAGIDTRRLTRILRDKGALAGCIVAGE 136
                                                  ************************************************************998866 PP

                                    TIGR01368 133 .sekeelvekakespkvkevnlvkevstkeayeleq.......k.akkegkklrvvvidlGvKeni 189
                                                   +++e + +ka++ p +++++l+k vs++++y++++       +  ++   + +vv++d+GvK ni
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714 137 hVDAEAALAKARAFPGLNGMDLAKVVSVTKPYAWKEgsydldrQaFEQPALRFKVVAYDYGVKFNI 202
                                                  1568889999*************************987766542345555569************* PP

                                    TIGR01368 190 lreLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclG 255
                                                  lr L+++g+++tvvpa+t+a+e+ +++pdg++lsnGPGdPaa+++a++ ++++l+akiP+fGIclG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714 203 LRLLAAQGCDITVVPAQTPAAEVLAMKPDGVFLSNGPGDPAACDYAVAATREFLDAKIPLFGICLG 268
                                                  ****************************************************************** PP

                                    TIGR01368 256 hqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgt 321
                                                  hq+++lalgakt+k+kfGh+GaNhpvkd+++grv itsqNHg+avd+++l+++ ++vth +l+Dg+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714 269 HQIMGLALGAKTLKMKFGHHGANHPVKDHDDGRVLITSQNHGFAVDPATLPAN-VRVTHSSLFDGS 333
                                                  *************************************************8866.************ PP

                                    TIGR01368 322 veglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                                  ++g + ++ p+f  Q HPeaspGphd  ylF++f +l++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2714 334 LQGFALTDRPAFCFQGHPEASPGPHDIGYLFERFAQLMQ 372
                                                  ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (375 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: 6.94
//
[ok]

This GapMind analysis is from Apr 09 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