Alignments for a candidate for carA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Burkholderia phytofirmans PsJN

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate BPHYT_RS14195 BPHYT_RS14195 carbamoyl phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__BFirm:BPHYT_RS14195
          Length = 384

 Score =  338 bits (867), Expect = 2e-97
 Identities = 174/376 (46%), Positives = 239/376 (63%), Gaps = 12/376 (3%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DG+++   S GAPG  I E+VFNT++TGYQEILTDPSYA Q V +T P IGN G
Sbjct: 8   ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVG 67

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           VN +D E+ +    GL+IR+L +  SN+R  +TL  YL +  ++ +  LDTR +TR LR+
Sbjct: 68  VNAEDVEATKVHAAGLIIRDLPVLASNFRMERTLPQYLQDEGVVAIAGLDTRMLTRVLRD 127

Query: 178 DGSLIGVLSTEQSKTDDE--LLQMSRSW-DIVGIDLISDVSCKSPYEWVDKTNAEWDFNT 234
            G+  G +    + +DDE   ++++RS+  + G+DL   VS K  YEW   T  EW    
Sbjct: 128 KGAQNGAI---LAGSDDEAKAIELARSFPGLSGMDLAKVVSTKETYEW---TQTEWRLGE 181

Query: 235 --NSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGP 292
              ++    Y+V+A+D+G+K NILR L+  GC +TV+P+   AA+AL +NPDGI  SNGP
Sbjct: 182 GYGTQKAPKYRVVAFDYGVKYNILRMLAERGCHVTVLPAQASAADALALNPDGIFLSNGP 241

Query: 293 GDPSAVPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRT 351
           GDP    YA+   KEL+ + +P +GIC+GHQ++G A+G KT KMK GHHG NHPV++   
Sbjct: 242 GDPEPCDYAITATKELIERGIPTFGICLGHQIMGLAVGAKTMKMKTGHHGANHPVKDLDD 301

Query: 352 GQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHD 411
           G+V I++QNH +AVD  +LP     THV+L DG+  G +  +      Q HPEASPGPHD
Sbjct: 302 GRVVITSQNHGFAVDADTLPANARATHVSLFDGTLQGFALTDKPAFCFQGHPEASPGPHD 361

Query: 412 SDNAFREFIELMKRSK 427
               F  F  LM   K
Sbjct: 362 IAYLFDRFTALMDTKK 377


Lambda     K      H
   0.316    0.134    0.403 

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: 469
Number of extensions: 16
Number of successful extensions: 4
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: 430
Length of database: 384
Length adjustment: 31
Effective length of query: 399
Effective length of database: 353
Effective search space:   140847
Effective search space used:   140847
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS14195 BPHYT_RS14195 (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.27590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.3e-147  476.1   0.0   3.8e-147  475.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS14195  BPHYT_RS14195 carbamoyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS14195  BPHYT_RS14195 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.9   0.0  3.8e-147  3.8e-147       1     360 [.       8     374 ..       8     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 475.9 bits;  conditional E-value: 3.8e-147
                                TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskk 70 
                                              a l+l+dGtvf+g+s+ga+++++GevvFnT++tGYqEiltDpsY++qiv+ltyp+ign+gvn+ed+e++k
  lcl|FitnessBrowser__BFirm:BPHYT_RS14195   8 ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVGVNAEDVEATK 77 
                                              579******************************************************************* PP

                                TIGR01368  71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelve 140
                                              ++++gl++++l   +sn+r++++L ++l++eg+vai+g+DTR+l++ lR+kg+++++i + + ++ +++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS14195  78 VHAAGLIIRDLPVLASNFRMERTLPQYLQDEGVVAIAGLDTRMLTRVLRDKGAQNGAILAGSDDEAKAIE 147
                                              ********************************************************************** PP

                                TIGR01368 141 kakespkvkevnlvkevstkeayeleq...k.....akkegkklrvvvidlGvKenilreLvkrgvevtv 202
                                               a++ p +++++l+k vstke+ye++q   +      +++  k+rvv++d+GvK nilr+L++rg++vtv
  lcl|FitnessBrowser__BFirm:BPHYT_RS14195 148 LARSFPGLSGMDLAKVVSTKETYEWTQtewRlgegyGTQKAPKYRVVAFDYGVKYNILRMLAERGCHVTV 217
                                              **************************966615556566777779************************** PP

                                TIGR01368 203 vpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkf 272
                                              +pa++sa++  +lnpdgi+lsnGPGdP+ +++ai+ +k+l+e+ iP+fGIclGhq+++la+gakt+k+k 
  lcl|FitnessBrowser__BFirm:BPHYT_RS14195 218 LPAQASAADALALNPDGIFLSNGPGDPEPCDYAITATKELIERGIPTFGICLGHQIMGLAVGAKTMKMKT 287
                                              ********************************************************************** PP

                                TIGR01368 273 GhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeas 342
                                              Gh+GaNhpvkdl++grv itsqNHg+avd ++l+++ +++thv+l+Dgt++g + +++p+f  Q HPeas
  lcl|FitnessBrowser__BFirm:BPHYT_RS14195 288 GHHGANHPVKDLDDGRVVITSQNHGFAVDADTLPAN-ARATHVSLFDGTLQGFALTDKPAFCFQGHPEAS 356
                                              ********************************8866.9******************************** PP

                                TIGR01368 343 pGphdteylFdefvelik 360
                                              pGphd +ylFd+f+ l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14195 357 PGPHDIAYLFDRFTALMD 374
                                              *************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (384 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.87
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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