GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Streptacidiphilus oryzae TH49

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_037573661.1 BS73_RS17765 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_000744815.1:WP_037573661.1
          Length = 372

 Score =  520 bits (1340), Expect = e-152
 Identities = 251/369 (68%), Positives = 297/369 (80%), Gaps = 1/369 (0%)

Query: 9   LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68
           +EIP+ +KP DGRFG+GPSKVR E L  L  T  +L GTSHRQAPVKNLV RVR G+A+L
Sbjct: 4   IEIPSDLKPADGRFGAGPSKVRPEALNALAATGTSLLGTSHRQAPVKNLVRRVREGVAQL 63

Query: 69  FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128
           FSLP+GY+V+LGNGG+TAFWD AA GL+ ++S HL++GEFS+KFA A    P++ +P II
Sbjct: 64  FSLPEGYQVVLGNGGSTAFWDVAAHGLVRRKSQHLSFGEFSSKFAKATKTAPWLADPTII 123

Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSD-DALVVIDATSGAGGLPVD 187
           TSDPG+ PE   +  VDV A+ HNETSTGVA+ + R  G+D DALV++DATSGAGGLPVD
Sbjct: 124 TSDPGTHPEAAAEAGVDVYAFTHNETSTGVAMPINRVAGADEDALVLVDATSGAGGLPVD 183

Query: 188 IAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKN 247
           I +TD YYFAPQKNFASDGGLW+   SPAAL R   IAA  R++P F  LP A++NS K+
Sbjct: 184 ITQTDVYYFAPQKNFASDGGLWIGAFSPAALDRAAEIAAGDRYIPAFFDLPTAIDNSAKD 243

Query: 248 QTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGL 307
           QTYNTP++ATL LLA+Q+DWL GNGGLDWA  RTADSS RLY WA++  YTTPFVTDP  
Sbjct: 244 QTYNTPSVATLFLLADQLDWLNGNGGLDWATARTADSSSRLYGWAEKTAYTTPFVTDPAK 303

Query: 308 RSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTE 367
           RSQV+GTIDF D VDA  VAK+LRANGIVDTEPYRKLGRNQLRVAMF A++P DV ALT 
Sbjct: 304 RSQVIGTIDFADSVDAAAVAKVLRANGIVDTEPYRKLGRNQLRVAMFAAIDPADVEALTA 363

Query: 368 CVDWVVERL 376
           C+D VVERL
Sbjct: 364 CIDHVVERL 372


Lambda     K      H
   0.317    0.134    0.399 

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: 523
Number of extensions: 14
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: 376
Length of database: 372
Length adjustment: 30
Effective length of query: 346
Effective length of database: 342
Effective search space:   118332
Effective search space used:   118332
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 WP_037573661.1 BS73_RS17765 (phosphoserine transaminase)
to HMM TIGR01366 (putative phosphoserine aminotransferase (EC 2.6.1.52))

# 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/TIGR01366.hmm
# target sequence database:        /tmp/gapView.3295256.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01366  [M=361]
Accession:   TIGR01366
Description: serC_3: putative phosphoserine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-209  681.8   3.1   1.3e-209  681.6   3.1    1.0  1  NCBI__GCF_000744815.1:WP_037573661.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037573661.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  681.6   3.1  1.3e-209  1.3e-209       1     361 []      11     372 .]      11     372 .] 1.00

  Alignments for each domain:
  == domain 1  score: 681.6 bits;  conditional E-value: 1.3e-209
                             TIGR01366   1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggatafw 73 
                                           kpadgrfgagpskvr+e+l+al+at++sllgtshrqa+vknlv +vreg+a+lfslp+gy+v+lgngg+tafw
  NCBI__GCF_000744815.1:WP_037573661.1  11 KPADGRFGAGPSKVRPEALNALAATGTSLLGTSHRQAPVKNLVRRVREGVAQLFSLPEGYQVVLGNGGSTAFW 83 
                                           7************************************************************************ PP

                             TIGR01366  74 daatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahnetstgvava 146
                                           d+a++gl+ +ks+hlsfgefsskfaka+k ap+l++p+i+t+dpg++pea ae+gvdv+a++hnetstgva++
  NCBI__GCF_000744815.1:WP_037573661.1  84 DVAAHGLVRRKSQHLSFGEFSSKFAKATKTAPWLADPTIITSDPGTHPEAAAEAGVDVYAFTHNETSTGVAMP 156
                                           ************************************************************************* PP

                             TIGR01366 147 vrrpegsde.alvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaaleriekiaasgrfvpe 218
                                           + r++g+de alv++datsgagglpvdi++tdvyyfapqk+fasdgglw++++spaal+r+ +iaa +r++p 
  NCBI__GCF_000744815.1:WP_037573661.1 157 INRVAGADEdALVLVDATSGAGGLPVDITQTDVYYFAPQKNFASDGGLWIGAFSPAALDRAAEIAAGDRYIPA 229
                                           *******988*************************************************************** PP

                             TIGR01366 219 flslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlyswaeereyatpfvadaa 291
                                           f++lpta+dns k+qtyntp+vatl+ll++q+dwlngnggld+a+art+dsssrly wae++ y+tpfv+d+a
  NCBI__GCF_000744815.1:WP_037573661.1 230 FFDLPTAIDNSAKDQTYNTPSVATLFLLADQLDWLNGNGGLDWATARTADSSSRLYGWAEKTAYTTPFVTDPA 302
                                           ************************************************************************* PP

                             TIGR01366 292 krsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpadvealteavdfvvekl 361
                                           krsqv+gtidf+d++daa+vak+lrangivdtepyrklgrnqlrvamf aidpadvealt ++d+vve+l
  NCBI__GCF_000744815.1:WP_037573661.1 303 KRSQVIGTIDFADSVDAAAVAKVLRANGIVDTEPYRKLGRNQLRVAMFAAIDPADVEALTACIDHVVERL 372
                                           ********************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (372 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: 12.53
//
[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