Aligments for a candidate for carA in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Aligments for a candidate for carA in Pseudomonas fluorescens FW300-N2E2

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate Pf6N2E2_3365 Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365
          Length = 378

 Score =  339 bits (870), Expect = 7e-98
 Identities = 175/376 (46%), Positives = 241/376 (64%), Gaps = 11/376 (2%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DGSI+  ++ GA G  + E+VFNT++TGYQEILTDPSYA Q V +T P IGNTG
Sbjct: 5   AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHIGNTG 64

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
             P+D ES + +  GLVIR+L +  SNWR T +L+DYL   +++ +  +DTR +TR LRE
Sbjct: 65  TTPEDAESDRVWSAGLVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGIDTRRLTRILRE 124

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSW-DIVGIDLISDVSCKSPYEWVDKTNAEWDFNTNS 236
            G+  G +    + +++  +  ++ +  + G+DL   VS K  YEW    +  WD  T+S
Sbjct: 125 KGAQNGCIMAGDNISEEAAIAAAQGFPGLKGMDLAKVVSTKKQYEW---RSTVWDLKTDS 181

Query: 237 R-----DGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNG 291
                     Y V+AYD+G+K NILR L   GC++TVVP+  PAA+ L + PDG+  SNG
Sbjct: 182 HATIEASELPYHVVAYDYGVKLNILRMLVERGCRVTVVPAQTPAADVLALKPDGVFLSNG 241

Query: 292 PGDPSAVPYAVETVKELL-GKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNR 350
           PGDP    YA++ +K++L  ++PV+GIC+GHQLL  A G KT KM  GHHG NHPV++  
Sbjct: 242 PGDPEPCDYAIQAIKDVLETEIPVFGICLGHQLLALASGAKTLKMGHGHHGANHPVQDLD 301

Query: 351 TGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPH 410
           TG V I++QNH +AVD A+LP  V   H +L DG+  G+   + +  S Q HPEASPGP+
Sbjct: 302 TGVVMITSQNHGFAVDEATLPANVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGPN 361

Query: 411 DSDNAFREFI-ELMKR 425
           D    F  FI E+ KR
Sbjct: 362 DVAPLFDRFISEMAKR 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: 443
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 430
Length of database: 378
Length adjustment: 31
Effective length of query: 399
Effective length of database: 347
Effective search space:   138453
Effective search space used:   138453
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 Pf6N2E2_3365 (Carbamoyl-phosphate synthase small chain (EC 6.3.5.5))
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.4164.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   6.4e-148  478.5   0.0   7.2e-148  478.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365  Carbamoyl-phosphate synthase sma


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365  Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.3   0.0  7.2e-148  7.2e-148       1     360 [.       5     375 ..       5     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 478.3 bits;  conditional E-value: 7.2e-148
                                      TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvnee 64 
                                                    a+l+l+dG++f+g+++ga++++vGevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+g+++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365   5 AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHIGNTGTTPE 68 
                                                    689************************************************************* PP

                                      TIGR01368  65 daeskkikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavi 128
                                                    daes++++ +glv+++l   +sn+r++ sL+++lk +++vai+g+DTR l++ lRekg+++++i
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365  69 DAESDRVWSAGLVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGIDTRRLTRILREKGAQNGCI 132
                                                    **************************************************************** PP

                                      TIGR01368 129 stekse.keelvekakespkvkevnlvkevstkeayeleq.........k..akkegkklrvvv 180
                                                    ++ ++  +e ++++a+  p +k+++l+k vstk++ye+++         +  +++++  ++vv+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365 133 MAGDNIsEEAAIAAAQGFPGLKGMDLAKVVSTKKQYEWRStvwdlktdsHatIEASELPYHVVA 196
                                                    99875526777888999**********************977777655414345555559**** PP

                                      TIGR01368 181 idlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklle 244
                                                    +d+GvK nilr+Lv+rg++vtvvpa+t+a+++ +l+pdg++lsnGPGdP+ +++ai+ +k +le
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365 197 YDYGVKLNILRMLVERGCRVTVVPAQTPAADVLALKPDGVFLSNGPGDPEPCDYAIQAIKDVLE 260
                                                    **************************************************************** PP

                                      TIGR01368 245 akiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkee 308
                                                    ++iP+fGIclGhqllala+gakt+k+  Gh+GaNhpv+dl+tg v+itsqNHg+avde++l+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365 261 TEIPVFGICLGHQLLALASGAKTLKMGHGHHGANHPVQDLDTGVVMITSQNHGFAVDEATLPAN 324
                                                    ************************************************************8866 PP

                                      TIGR01368 309 elevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                                     +++ h++l+Dgt++g+e++++ +fs Q HPeaspGp+d + lFd+f+++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3365 325 -VRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGPNDVAPLFDRFISEMA 375
                                                    .***********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (378 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: 9.55
//
[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