GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2C3

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO356_25400 AO356_25400 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25400
          Length = 389

 Score =  285 bits (730), Expect = 1e-81
 Identities = 145/379 (38%), Positives = 226/379 (59%), Gaps = 10/379 (2%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           +++  +L +LV F +V    N  ++ ++R YL+  G+  +++   E  ++N+ A+IGP  
Sbjct: 4   LRSRALLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAERTKANLLASIGPAL 63

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
             G ++SGH DVVP     WT +PF L     + +GRGT DMKG+LA+VLAAVP   + P
Sbjct: 64  PGGVVLSGHTDVVPVDGQAWTVEPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSP 123

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180
           LRRP+HLA SYDEE GC GV  ++  LP+   QP   +IGEPT ++ +  HKGK A R  
Sbjct: 124 LRRPVHLAFSYDEEVGCLGVRSLLEVLPQRIAQPALCLIGEPTELQPVLGHKGKLAMRCH 183

Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKG 238
           V+G + HS+    G+NAI   A ++ + + E    +  P  H   F+P +S++Q+G V G
Sbjct: 184 VKGAACHSAYAPYGVNAIEQAARLIGR-LGEIGAQLAEPSRHDPRFDPAFSTVQVGVVHG 242

Query: 239 GQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFE-------VEWQELSA 291
           G A+NI+P  C  +FE RA+   DP  +   ++  AE       +       + ++ LSA
Sbjct: 243 GTALNIVPADCRFDFEVRALPDFDPLVVAEQLQGYAEQTLLPAMQAVAGDTAIRFEPLSA 302

Query: 292 YPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE 351
           YP L+  PD+  A L+  L G +A   V++GTE GLF +AG+  ++CGPG + + HKPDE
Sbjct: 303 YPGLATSPDSAAAQLVARLCGSDAFSTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDE 362

Query: 352 YILIDELMACRAMVEALGA 370
           Y+ ++++ AC  +++ L +
Sbjct: 363 YVSVEQMAACDRLMDRLAS 381


Lambda     K      H
   0.319    0.137    0.410 

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: 402
Number of extensions: 10
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: 374
Length of database: 389
Length adjustment: 30
Effective length of query: 344
Effective length of database: 359
Effective search space:   123496
Effective search space used:   123496
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 AO356_25400 AO356_25400 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

# 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/TIGR01892.hmm
# target sequence database:        /tmp/gapView.28640.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01892  [M=365]
Accession:   TIGR01892
Description: AcOrn-deacetyl: acetylornithine deacetylase (ArgE)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.3e-125  405.2   0.0   1.4e-125  405.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400  AO356_25400 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400  AO356_25400 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.1   0.0  1.4e-125  1.4e-125       2     364 ..       9     379 ..       8     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.1 bits;  conditional E-value: 1.4e-125
                                       TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvl 64 
                                                     +la+Lv+f +vs+ sn++lie+v+dyl+ lgv+ e + +a+  +k nlla+iGp+   gg+vl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400   9 LLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAER-TKANLLASIGPAL-PGGVVL 69 
                                                     689*************************************99.************9.9***** PP

                                       TIGR01892  65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvl 127
                                                     sGhtDvvPvd++aWt +pf Lte dg+ +grGtaDmkG+la vLaavp     +L++P+hl++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400  70 SGHTDVVPVDGQAWTVEPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSPLRRPVHLAF 132
                                                     *************************************************************** PP

                                       TIGR01892 128 saDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpd 187
                                                     s+Deevg++G+++l+e+l+    +pal ++GePt+l++v  hkGk +++ +v+G   hs+++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 133 SYDEEVGCLGVRSLLEVLPqriAQPALCLIGEPTELQPVLGHKGKLAMRCHVKGAACHSAYAP 195
                                                     ******************988889*************************************** PP

                                       TIGR01892 188 rGvsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvle 249
                                                      Gv+aie+aa+l++rl +   +l + + ++  F+p ++t+++G+v+GG+a ni++a C++ +e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 196 YGVNAIEQAARLIGRLGEIGAQLAEpSRHDPRFDPAFSTVQVGVVHGGTALNIVPADCRFDFE 258
                                                     ************************98999********************************** PP

                                       TIGR01892 250 lRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvallekl 307
                                                     +R++p  dp  + ++l+  ae+     +++ a ++ ++ e lsa+p+l++ +d+ +++l+++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 259 VRALPDFDPLVVAEQLQGYAEQtllpaMQAVAGDTAIRFEPLSAYPGLATSPDSAAAQLVARL 321
                                                     ****************99998877765555566677788999********************* PP

                                       TIGR01892 308 aGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                      G+ a  +v++gte gl+ ++G+++vv+GPG++dq h+pdeYv +e++ +c+ l+ rl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 322 CGSdAFSTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEYVSVEQMAACDRLMDRL 379
                                                     **9999*************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (389 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: 10.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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