GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Lentibacillus jeotgali Grbi

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_010530473.1 ON01_RS07815 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_000224785.1:WP_010530473.1
          Length = 364

 Score =  451 bits (1159), Expect = e-131
 Identities = 216/358 (60%), Positives = 275/358 (76%), Gaps = 3/358 (0%)

Query: 2   KRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGNY 61
           +R+L+LE+  +F GE FG+     GEVVFNTGMTGYQE+++DPSYCGQ+V +TYPLIGNY
Sbjct: 3   ERQLILEDSTIFTGEGFGADISATGEVVFNTGMTGYQEVITDPSYCGQMVVMTYPLIGNY 62

Query: 62  GINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMIR 121
           GINRDDFE++TPF+ GLI+KE  E PSN+RS  TL +YLK   IPG+ G+DTRKLT++IR
Sbjct: 63  GINRDDFETVTPFIHGLIVKEFSEFPSNFRSDETLHDYLKANGIPGISGLDTRKLTKIIR 122

Query: 122 TAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFGMKH 181
             G +K   A +    E +++ L       +QV+Q S    Y  PGRGKRIVLVDFGMKH
Sbjct: 123 KHGTMKAIMADAGMPAEELIESLKGLPDQTDQVNQTSTIKPYVVPGRGKRIVLVDFGMKH 182

Query: 182 GILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLGKVP 241
            ILREL KR C V VVPYN +A ++L+LKPDGIML+NGPGDPK+VPE+IEM++ VLGK+P
Sbjct: 183 SILRELTKRDCHVTVVPYNYSAGDILRLKPDGIMLTNGPGDPKNVPESIEMVQTVLGKIP 242

Query: 242 LFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTVS--SISKT 299
           LFGICLGHQLFALACGA+T+KM FGHRG N PVK+    K  +TSQNH Y V+  S+  T
Sbjct: 243 LFGICLGHQLFALACGADTKKMAFGHRGVNQPVKDTEKNKTFMTSQNHSYAVTHDSLIGT 302

Query: 300 ELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMI-ETTEKE 356
           +L++   ++ND+++EG++H T PAF+VQYHPE+SPGPED   LFD F++MI E  +KE
Sbjct: 303 DLDLIQFSLNDNSVEGIRHLTYPAFSVQYHPESSPGPEDTPQLFDEFLQMISEFRQKE 360


Lambda     K      H
   0.317    0.136    0.397 

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: 441
Number of extensions: 10
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: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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: 49 (23.5 bits)

Align candidate WP_010530473.1 ON01_RS07815 (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.3341405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-145  469.4   0.0   4.1e-145  469.2   0.0    1.0  1  NCBI__GCF_000224785.1:WP_010530473.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010530473.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2   0.0  4.1e-145  4.1e-145       2     360 ..       5     354 ..       4     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 4.1e-145
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                           +l+led t+f+g++fga+ +++GevvFnT+mtGYqE++tDpsY gq+vv+typlignyg+n++d+e  ++ ++
  NCBI__GCF_000224785.1:WP_010530473.1   5 QLILEDSTIFTGEGFGADISATGEVVFNTGMTGYQEVITDPSYCGQMVVMTYPLIGNYGINRDDFETVTPFIH 77 
                                           699********************************************************************** PP

                             TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespk 147
                                           gl+vke+s+ +sn+r+ e+L+++lk +gi++i g+DTR+l+k +R++g+mka+++++ + +eel+e++k  p+
  NCBI__GCF_000224785.1:WP_010530473.1  78 GLIVKEFSEFPSNFRSDETLHDYLKANGIPGISGLDTRKLTKIIRKHGTMKAIMADAGMPAEELIESLKGLPD 150
                                           *******************************************************************999999 PP

                             TIGR01368 148 vkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220
                                            +  + v++ st ++y +      +gk  r+v++d+G+K++ilreL+kr+++vtvvp+++sa +i +l+pdgi
  NCBI__GCF_000224785.1:WP_010530473.1 151 QT--DQVNQTSTIKPYVVPG----RGK--RIVLVDFGMKHSILRELTKRDCHVTVVPYNYSAGDILRLKPDGI 215
                                           97..99**********9994....344..6******************************************* PP

                             TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveits 293
                                           +l+nGPGdP++v e ie+v+++l+ kiP+fGIclGhql+ala ga+t k+ fGhrG N+pvkd+++++ ++ts
  NCBI__GCF_000224785.1:WP_010530473.1 216 MLTNGPGDPKNVPESIEMVQTVLG-KIPLFGICLGHQLFALACGADTKKMAFGHRGVNQPVKDTEKNKTFMTS 287
                                           ************************.************************************************ PP

                             TIGR01368 294 qNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                           qNH+yav ++sl  ++l+  + +lnD++veg++h ++p+fsvQyHPe+spGp+dt +lFdef+++i+
  NCBI__GCF_000224785.1:WP_010530473.1 288 QNHSYAVTHDSLIGTDLDLIQFSLNDNSVEGIRHLTYPAFSVQYHPESSPGPEDTPQLFDEFLQMIS 354
                                           ****************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (364 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.41
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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