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

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.5021.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.65
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis