GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Phyllobacterium endophyticum PEPV15

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_106719069.1 CU100_RS23480 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>NCBI__GCF_003010935.1:WP_106719069.1
          Length = 374

 Score =  271 bits (694), Expect = 2e-77
 Identities = 157/347 (45%), Positives = 211/347 (60%), Gaps = 10/347 (2%)

Query: 80  APTIVDVDLGDRSYPIYIGSGLLDQPDL-LQRHVHGKRVLVVTNSTVAPIYLDKVVGALT 138
           A T V V LGDRSY I IG+GL+D+    +       RV +V++ TVA ++LD++  +L+
Sbjct: 6   AITTVPVKLGDRSYDILIGAGLIDRAGAAIASRAGSVRVAIVSDETVAALHLDRLTRSLS 65

Query: 139 NGNPNVSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAA 198
                +    +++  GEK K   TL  V +  + +RL+R    +A GGGVIGD+ G+AA 
Sbjct: 66  GAG--IDSTPILVTAGEKSKGFATLEAVTNAILAARLERGDVVIAFGGGVIGDLAGFAAG 123

Query: 199 SFLRGVNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLPDR 258
              RG+ FIQ+PT+++AQVDSSVGGKTGIN   GKNL+G FYQPQ VL DTD L+TL  R
Sbjct: 124 IARRGMRFIQMPTSLLAQVDSSVGGKTGINTAHGKNLVGVFYQPQLVLADTDVLDTLTPR 183

Query: 259 ELASGLAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDEKE 318
           E  +G AEV KYGLI  ++FF W EKN   +    P     AI  SC++KA+VV+ DEKE
Sbjct: 184 EFRAGYAEVAKYGLIDRSDFFAWLEKNWRGIFDGGPER-TEAIAVSCQSKADVVARDEKE 242

Query: 319 SGLRATLNLGHTFGHAIETGFGY--GQWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRAH 376
           +G RA LNLGHTFGHA+ET   Y   + +HGE V+ G+V+A   S ++    +    R  
Sbjct: 243 TGDRALLNLGHTFGHALETATNYDSARLVHGEGVSIGIVLAHQFSTKMNLASQDDAGRVE 302

Query: 377 NILQQAKLPTA----PPETMTVEMFKSVMAVDKKVADGLLRLILLKG 419
              +Q  LP +    P E  + E     +A DKKVA G L  IL +G
Sbjct: 303 AHFRQVGLPVSIGDIPGELPSAEKLMDYIAQDKKVARGALTFILTRG 349


Lambda     K      H
   0.318    0.133    0.385 

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: 375
Number of extensions: 14
Number of successful extensions: 5
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: 445
Length of database: 374
Length adjustment: 31
Effective length of query: 414
Effective length of database: 343
Effective search space:   142002
Effective search space used:   142002
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_106719069.1 CU100_RS23480 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.72195.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-106  341.7   0.0   2.9e-106  341.5   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106719069.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106719069.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.5   0.0  2.9e-106  2.9e-106       1     341 [.      19     366 ..      19     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 341.5 bits;  conditional E-value: 2.9e-106
                             TIGR01357   1 ykvkvgegllkklveelaeka..sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakl 71 
                                           y++ +g gl++++ +++a++a   ++ +++de+v++l+ ++l + l+ +g+  + ++v +ge+sK ++t++++
  NCBI__GCF_003010935.1:WP_106719069.1  19 YDILIGAGLIDRAGAAIASRAgsVRVAIVSDETVAALHLDRLTRSLSGAGIDSTPILVTAGEKSKGFATLEAV 91 
                                           6899*******999999995545899*********************************************** PP

                             TIGR01357  72 ldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGaf 144
                                           ++++l++ ler +v++a+GGGv+gDlaGF+A +  RG+r++q+PT+lla+vDssvGGKtgin+++gkNl+G f
  NCBI__GCF_003010935.1:WP_106719069.1  92 TNAILAARLERGDVVIAFGGGVIGDLAGFAAGIARRGMRFIQMPTSLLAQVDSSVGGKTGINTAHGKNLVGVF 164
                                           ************************************************************************* PP

                             TIGR01357 145 yqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaev 217
                                           yqP++Vl d++vl tl+ re+r+G+aEv K+gli  +++f++lekn++ + +       +e+i+ s++ Ka+v
  NCBI__GCF_003010935.1:WP_106719069.1 165 YQPQLVLADTDVLDTLTPREFRAGYAEVAKYGLIDRSDFFAWLEKNWRGIFD--GGPERTEAIAVSCQSKADV 235
                                           ***********************************************98775..67999************** PP

                             TIGR01357 218 VeeDekesglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgllkaellerlvallkkl 287
                                           V++Deke+g RalLN+GHt+gHa+E++++y+   l HGe V+iG+v++ ++s k+ l++++++ r++a ++++
  NCBI__GCF_003010935.1:WP_106719069.1 236 VARDEKETGDRALLNLGHTFGHALETATNYDsarLVHGEGVSIGIVLAHQFSTKMNLASQDDAGRVEAHFRQV 308
                                           ******************************99999************************************** PP

                             TIGR01357 288 glptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                           glp+++ +      s+e+l++++ +DKK  ++ ++++l + iG+a++a++v+ +++l+
  NCBI__GCF_003010935.1:WP_106719069.1 309 GLPVSIGDipgeLPSAEKLMDYIAQDKKVARGALTFILTRGIGQAFIAKDVPPSAVLS 366
                                           ******9999977899********************************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (374 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: 18.86
//
[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