GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Streptacidiphilus oryzae TH49

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_084704115.1 BS73_RS16265 succinyldiaminopimelate transaminase

Query= BRENDA::Q82IK5
         (364 letters)



>NCBI__GCF_000744815.1:WP_084704115.1
          Length = 390

 Score =  548 bits (1411), Expect = e-160
 Identities = 274/365 (75%), Positives = 304/365 (83%), Gaps = 5/365 (1%)

Query: 4   VSDRLPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPGYPTVW 63
           VS  LP FPWD+LEPYK RA  HPDGIVDLS+GTPVDPVP LIQ+AL   AD+PGYPTVW
Sbjct: 22  VSALLPQFPWDRLEPYKKRALEHPDGIVDLSIGTPVDPVPALIQEALREHADTPGYPTVW 81

Query: 64  GTPELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYP 123
           GT   RDA+ GW  RRLGA  +  H VLP+VGSKELVAWLPTQLGLGPGD VA+P+LAYP
Sbjct: 82  GTRAYRDAILGWAGRRLGATALDEHGVLPVVGSKELVAWLPTQLGLGPGDVVAYPQLAYP 141

Query: 124 TYEVGARLARADHVVY-DDPTELDP---TGLKLLWLNSPSNPTGKVLSKAELTRIVAWAR 179
           TYEVGARLARAD+  Y DDP ELD    + L+LLWLNSPSNPTG+VL+   L  IV WAR
Sbjct: 142 TYEVGARLARADYASYVDDPRELDADVVSRLRLLWLNSPSNPTGRVLAADRLREIVEWAR 201

Query: 180 EHGILVFSDECYLELGWEADPVSVLHPDVCGGSYEGIVSVHSLSKRSNLAGYRAAFLAGD 239
           E G+LV SDECYLELGWEADPVS+LHP+V GGSYEG+V+VHSLSKRSNLAGYRAAFL GD
Sbjct: 202 ERGVLVVSDECYLELGWEADPVSILHPEVSGGSYEGLVAVHSLSKRSNLAGYRAAFLLGD 261

Query: 240 PAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAARRTALRDALLSHGFR 299
             +L  LLQ+RKHGGMMT AP QAA   ALGDDAHV EQRERYA RRTALR+AL ++GFR
Sbjct: 262 DGLLHELLQVRKHGGMMTPAPVQAAAAVALGDDAHVAEQRERYARRRTALREALEAYGFR 321

Query: 300 IEHSEASLYLWATRGESCWDTVAHLADLGILVAPGDFYGS-AGEQFVRVALTATDERVAA 358
           ++HSEASLYLW+TR ESCWDTVA LADLGILVAPG+FYG+ AG + VRVA TATDERV A
Sbjct: 322 VDHSEASLYLWSTRDESCWDTVAALADLGILVAPGEFYGAEAGSRHVRVAFTATDERVDA 381

Query: 359 AVRRL 363
           AV RL
Sbjct: 382 AVIRL 386


Lambda     K      H
   0.319    0.135    0.420 

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: 615
Number of extensions: 26
Number of successful extensions: 3
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: 390
Length adjustment: 30
Effective length of query: 334
Effective length of database: 360
Effective search space:   120240
Effective search space used:   120240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_084704115.1 BS73_RS16265 (succinyldiaminopimelate transaminase)
to HMM TIGR03539 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

# 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/TIGR03539.hmm
# target sequence database:        /tmp/gapView.3923009.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03539  [M=357]
Accession:   TIGR03539
Description: DapC_actino: succinyldiaminopimelate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-180  586.3   0.7   1.2e-180  586.1   0.7    1.0  1  NCBI__GCF_000744815.1:WP_084704115.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_084704115.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.1   0.7  1.2e-180  1.2e-180       1     357 []      26     387 ..      26     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 586.1 bits;  conditional E-value: 1.2e-180
                             TIGR03539   1 lPdfPWdklaeakakaashpdGivdlsvGtPvdpvpalirealaeaadapgyPqtaGteelreaivdalerrl 73 
                                           lP+fPWd+l+++k++a +hpdGivdls+GtPvdpvpali+eal e ad+pgyP+++Gt++ r+ai+++  rrl
  NCBI__GCF_000744815.1:WP_084704115.1  26 LPQFPWDRLEPYKKRALEHPDGIVDLSIGTPVDPVPALIQEALREHADTPGYPTVWGTRAYRDAILGWAGRRL 98 
                                           8************************************************************************ PP

                             TIGR03539  74 gvkgldeeavlPviGtkelvallPtllGlgagdtvviPevayPtyevgarlagaeava.addlteldp...ek 142
                                           g+++lde+ vlPv+G+kelva+lPt+lGlg+gd+v+ P++ayPtyevgarla+a+  + +dd++eld    ++
  NCBI__GCF_000744815.1:WP_084704115.1  99 GATALDEHGVLPVVGSKELVAWLPTQLGLGPGDVVAYPQLAYPTYEVGARLARADYASyVDDPRELDAdvvSR 171
                                           ******************************************************987527******9966668 PP

                             TIGR03539 143 vkliwlnsPanPtGrvlsveelrkvvalarergvvvasdecylelgWegeavsvldpevcggdlegllavhsl 215
                                           ++l+wlnsP+nPtGrvl  ++lr++v++arergv+v+sdecylelgWe+++vs+l+pev+gg++egl+avhsl
  NCBI__GCF_000744815.1:WP_084704115.1 172 LRLLWLNSPSNPTGRVLAADRLREIVEWARERGVLVVSDECYLELGWEADPVSILHPEVSGGSYEGLVAVHSL 244
                                           89*********************************************************************** PP

                             TIGR03539 216 skrsnlagyragfvaGdealvaellevrkhaGlmvpaPvqaamvaaladdehvaeqkeryaarrellkaalek 288
                                           skrsnlagyra+f+ Gd+ l++ell+vrkh+G+m+paPvqaa ++al+dd+hvaeq+erya+rr++l++ale+
  NCBI__GCF_000744815.1:WP_084704115.1 245 SKRSNLAGYRAAFLLGDDGLLHELLQVRKHGGMMTPAPVQAAAAVALGDDAHVAEQRERYARRRTALREALEA 317
                                           ************************************************************************* PP

                             TIGR03539 289 aGfriehseaglylWatrgedaretvdrlaelGilvaPGdfyg.eagkefvrvaltatderiaaaverlt 357
                                           +Gfr++hsea+lylW+tr+e++++tv++la+lGilvaPG+fyg eag+++vrva+tatder++aav rlt
  NCBI__GCF_000744815.1:WP_084704115.1 318 YGFRVDHSEASLYLWSTRDESCWDTVAALADLGILVAPGEFYGaEAGSRHVRVAFTATDERVDAAVIRLT 387
                                           ******************************************934689********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (390 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: 00:00:00.00
# Mc/sec: 14.18
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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