GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB in Shewanella loihica PV-4

Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate 5208569 Shew_1080 homoserine kinase (RefSeq)

Query= CharProtDB::CH_002113
         (310 letters)



>FitnessBrowser__PV4:5208569
          Length = 316

 Score =  352 bits (903), Expect = e-102
 Identities = 172/304 (56%), Positives = 222/304 (73%), Gaps = 1/304 (0%)

Query: 4   VYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAA-ETFSLNNLGRFADKLPSEPRE 62
           VYAPAS  N+ VGFD+LGAA+ PVDG LLGD V +E+A    SL+  G +ADKLP+   E
Sbjct: 5   VYAPASMGNVGVGFDLLGAALAPVDGCLLGDRVAIESAPHGVSLSLAGHWADKLPAASEE 64

Query: 63  NIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTR 122
           NIVYQC   F ++LG +  VAMTLEKN+P+GSGLGSSA SVVAAL A+NEH  +P +   
Sbjct: 65  NIVYQCATFFLEQLGSRAGVAMTLEKNLPVGSGLGSSASSVVAALYALNEHFDRPYDSDA 124

Query: 123 LLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKV 182
           LL LMGE EG+ISGS+HYDNVAPC+LGGMQLM++    + Q +P F +W WV+AYPGI +
Sbjct: 125 LLRLMGEFEGKISGSVHYDNVAPCYLGGMQLMLDTPSAVCQGLPVFKDWYWVVAYPGISL 184

Query: 183 STAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPGF 242
           STA+ RA+LPAQY +   I  GR+L+ F+HA Y +  +LA +++KDV+AEPYR   +PG+
Sbjct: 185 STAKMRALLPAQYDKSVAIDFGRYLSAFVHASYRQDAKLAIEVLKDVLAEPYRASEIPGY 244

Query: 243 RQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLDT 302
            QAR A+ E+G   +GISGSGPTLF++ D  ETA +   WL  NY+ +  GF HIC++D 
Sbjct: 245 EQARAALDELGMATTGISGSGPTLFSVTDNLETANKAKAWLDANYVTSGSGFSHICQIDM 304

Query: 303 AGAR 306
            G R
Sbjct: 305 LGTR 308


Lambda     K      H
   0.321    0.136    0.412 

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: 307
Number of extensions: 6
Number of successful extensions: 2
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: 316
Length adjustment: 27
Effective length of query: 283
Effective length of database: 289
Effective search space:    81787
Effective search space used:    81787
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 5208569 Shew_1080 (homoserine kinase (RefSeq))
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.26175.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
      7e-90  286.9   0.0    7.8e-90  286.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208569  Shew_1080 homoserine kinase (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208569  Shew_1080 homoserine kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.7   0.0   7.8e-90   7.8e-90       1     300 [.       3     308 ..       3     312 .. 0.98

  Alignments for each domain:
  == domain 1  score: 286.7 bits;  conditional E-value: 7.8e-90
                        TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk..sleaegegvekipkesdkNliyqvakkvlkklgk 76 
                                      l+v++Pas  N+g+GfD lG+al +v+++l+++ va+es+ +  sl  +g+ ++k+p+ s++N++yq+a+ +l++lg 
  lcl|FitnessBrowser__PV4:5208569   3 LTVYAPASMGNVGVGFDLLGAALAPVDGCLLGDRVAIESAPHgvSLSLAGHWADKLPAASEENIVYQCATFFLEQLGS 80 
                                      68***********************************9999999********************************** PP

                        TIGR00191  77 rvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlqlav 148
                                      r  +v++t+ek++p+g+GLGSSa+++vaa++a+ne+++ +++   ll l+++ Eg      H+DNvap++lGG+ql++
  lcl|FitnessBrowser__PV4:5208569  81 R-AGVAMTLEKNLPVGSGLGSSASSVVAALYALNEHFDRPYDSDALLRLMGEFEGkisgsvHYDNVAPCYLGGMQLML 157
                                      *.**************************************************************************** PP

                        TIGR00191 149 keddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkDrvh 226
                                           ++++ +P ++++++v+++P+i++sTa+ Ra+LP++y+ + ++  ++ l+ +v+A + +  a+l+  ++kD+++
  lcl|FitnessBrowser__PV4:5208569 158 DTPS-AVCQGLPVFKDWYWVVAYPGISLSTAKMRALLPAQYDKSVAIDFGRYLSAFVHASYRQ-DAKLAIEVLKDVLA 233
                                      *999.**********************************************************.89999999****** PP

                        TIGR00191 227 qpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakegieltvkvleldtdgae 300
                                      +pyR++ iP++++ + a  e g+ ++++SG+Gpt+++++++ + ++ka+ +l+ ++     ++++++++d+ g++
  lcl|FitnessBrowser__PV4:5208569 234 EPYRASEIPGYEQARAALDELGMATTGISGSGPTLFSVTDNLEtANKAKAWLDANYVTSGSGFSHICQIDMLGTR 308
                                      ******************************************99**************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (316 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: 9.69
//
[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