GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB in Pedobacter sp. GW460-11-11-14-LB5

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate CA265_RS23470 CA265_RS23470 homoserine kinase

Query= reanno::Pedo557:CA265_RS23470
         (310 letters)



>FitnessBrowser__Pedo557:CA265_RS23470
          Length = 310

 Score =  610 bits (1573), Expect = e-179
 Identities = 310/310 (100%), Positives = 310/310 (100%)

Query: 1   MKDSIKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTDTPGVVIKGITGDDGRLPLDA 60
           MKDSIKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTDTPGVVIKGITGDDGRLPLDA
Sbjct: 1   MKDSIKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTDTPGVVIKGITGDDGRLPLDA 60

Query: 61  AKNTVSASVQHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLS 120
           AKNTVSASVQHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLS
Sbjct: 61  AKNTVSASVQHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLS 120

Query: 121 TKELVPFAMKGEELACGYGHADNVAPALLGGFVLVRSYDPLDVISLPTPAGMYAAIVYPE 180
           TKELVPFAMKGEELACGYGHADNVAPALLGGFVLVRSYDPLDVISLPTPAGMYAAIVYPE
Sbjct: 121 TKELVPFAMKGEELACGYGHADNVAPALLGGFVLVRSYDPLDVISLPTPAGMYAAIVYPE 180

Query: 181 VDVPTKDARQMIRSKVALKDAVTQWGNVAGLVSGLFMNDFDLIGRSMKDVLVEPTRSILI 240
           VDVPTKDARQMIRSKVALKDAVTQWGNVAGLVSGLFMNDFDLIGRSMKDVLVEPTRSILI
Sbjct: 181 VDVPTKDARQMIRSKVALKDAVTQWGNVAGLVSGLFMNDFDLIGRSMKDVLVEPTRSILI 240

Query: 241 PGFEEMRKLAMENGAIGFGISGSGPSVFSLTKDEETARKITKSQQQHLHKININSKAFVS 300
           PGFEEMRKLAMENGAIGFGISGSGPSVFSLTKDEETARKITKSQQQHLHKININSKAFVS
Sbjct: 241 PGFEEMRKLAMENGAIGFGISGSGPSVFSLTKDEETARKITKSQQQHLHKININSKAFVS 300

Query: 301 PVNAEGPKVL 310
           PVNAEGPKVL
Sbjct: 301 PVNAEGPKVL 310


Lambda     K      H
   0.317    0.136    0.388 

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: 558
Number of extensions: 17
Number of successful extensions: 1
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: 310
Length of database: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
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: 48 (23.1 bits)

Align candidate CA265_RS23470 CA265_RS23470 (homoserine kinase)
to HMM TIGR00191 (thrB: homoserine kinase (EC 2.7.1.39))

# 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/TIGR00191.hmm
# target sequence database:        /tmp/gapView.8155.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00191  [M=304]
Accession:   TIGR00191
Description: thrB: homoserine kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    5.6e-70  221.5   0.0    6.2e-70  221.4   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS23470  CA265_RS23470 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS23470  CA265_RS23470 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.4   0.0   6.2e-70   6.2e-70       1     297 [.       5     305 ..       5     310 .] 0.88

  Alignments for each domain:
  == domain 1  score: 221.4 bits;  conditional E-value: 6.2e-70
                                  TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedv.aqeskdksleaegegvekipkesdkNliyqva 67 
                                                +kv +Pa+ AN+  GfDvlG a+++  + + +  + +  +    ++  + +  ++p+++ kN +   +
  lcl|FitnessBrowser__Pedo557:CA265_RS23470   5 IKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTdTPGV---VIKGITGDDGRLPLDAAKNTVSASV 69 
                                                5899********************9988777773312222...34444444489************** PP

                                  TIGR00191  68 kkvlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg.... 131
                                                ++ lk+ ++   +v+++++k++p+g+GLGSS+a+ va++ a+n+l+g  ls++el+ +a+  E+    
  lcl|FitnessBrowser__Pedo557:CA265_RS23470  70 QHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLSTKELVPFAMKGEElacg 137
                                                ******99999****************************************************99*** PP

                                  TIGR00191 132 ..HpDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfn 197
                                                  H+DNvapallGG++l+ ++d  l v+++P+ + +++ +v+P+++v T++aR+++  ++ ++d+v +
  lcl|FitnessBrowser__Pedo557:CA265_RS23470 138 ygHADNVAPALLGGFVLVRSYDP-LDVISLPTPAGMYAAIVYPEVDVPTKDARQMIRSKVALKDAVTQ 204
                                                **********************9.999999999*********************************** PP

                                  TIGR00191 198 lshlavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilala 265
                                                  ++a+lv  l ++   dl+   mkD++ +p R+ liP+++e+++ a e+ga+g ++SG+Gp++++l+
  lcl|FitnessBrowser__Pedo557:CA265_RS23470 205 WGNVAGLVSGLFMN-DFDLIGRSMKDVLVEPTRSILIPGFEEMRKLAMENGAIGFGISGSGPSVFSLT 271
                                                **************.899999*********************************************** PP

                                  TIGR00191 266 eeek.eeka.qelleklakegieltvkvleldtd 297
                                                ++e+ ++k  ++  ++l+k +i+ +  v  ++ +
  lcl|FitnessBrowser__Pedo557:CA265_RS23470 272 KDEEtARKItKSQQQHLHKININSKAFVSPVNAE 305
                                                **99644430333444444444444444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (310 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.80
//
[ok]

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