Alignments for a candidate for thrB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Shewanella oneidensis MR-1

Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate 202521 SO3414 homoserine kinase (NCBI ptt file)

Query= CharProtDB::CH_002113
         (310 letters)



>FitnessBrowser__MR1:202521
          Length = 312

 Score =  342 bits (877), Expect = 7e-99
 Identities = 170/305 (55%), Positives = 219/305 (71%), Gaps = 2/305 (0%)

Query: 4   VYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAET-FSLNNLGRFADKLPSEPRE 62
           VYAPAS  N+ VGFD+LGAA+ P+DG+LLGD VT+ AA+   SL  +G +A KLPS P +
Sbjct: 5   VYAPASMGNVGVGFDLLGAALAPIDGSLLGDRVTIAAADGGVSLTQVGGWAHKLPSNPED 64

Query: 63  NIVYQCWERFCQELGKQIP-VAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDT 121
           NIV+QC   F + LGK+   VA+TLEKN+P+GSGLGSSA SVVAAL A+NEH G P +  
Sbjct: 65  NIVHQCAVFFLKALGKENRGVALTLEKNLPVGSGLGSSASSVVAALYALNEHFGCPYDKQ 124

Query: 122 RLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIK 181
            LL LMGE EG+ISGS+HYDNVAPC+LGGMQLM+     I + +P F +W WV+AYPGI 
Sbjct: 125 ALLELMGEFEGKISGSVHYDNVAPCYLGGMQLMLNVPGAICEAIPSFKQWYWVVAYPGIS 184

Query: 182 VSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPG 241
           +STA  R ++P QY +   I  GR+L+ F+HA Y +  +LA +++KDV+AEPYR   +PG
Sbjct: 185 LSTAMMRKLMPEQYDKSVVIDFGRYLSAFVHASYQQNAQLAIQVLKDVLAEPYRAAAIPG 244

Query: 242 FRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLD 301
           +  AR A+AE+G + +GISGSGPTLF++ D   TA     WL  NYL +  GF H+CRLD
Sbjct: 245 YDNARAALAELGMLTTGISGSGPTLFSVTDDLATANAAKAWLEANYLTDAGGFAHVCRLD 304

Query: 302 TAGAR 306
             G R
Sbjct: 305 EQGTR 309


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: 291
Number of extensions: 9
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: 310
Length of database: 312
Length adjustment: 27
Effective length of query: 283
Effective length of database: 285
Effective search space:    80655
Effective search space used:    80655
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 202521 SO3414 (homoserine kinase (NCBI ptt file))
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.14387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    2.4e-91  291.7   0.0    2.7e-91  291.5   0.0    1.0  1  lcl|FitnessBrowser__MR1:202521  SO3414 homoserine kinase (NCBI p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202521  SO3414 homoserine kinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.5   0.0   2.7e-91   2.7e-91       1     300 [.       3     309 ..       3     312 .] 0.98

  Alignments for each domain:
  == domain 1  score: 291.5 bits;  conditional E-value: 2.7e-91
                       TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk..sleaegegvekipkesdkNliyqvakkvlkklgkr 77 
                                     l+v++Pas  N+g+GfD lG+al +++++l+++ v+++++d   sl+++g  ++k+p+++++N++ q+a+ +lk lgk+
  lcl|FitnessBrowser__MR1:202521   3 LTVYAPASMGNVGVGFDLLGAALAPIDGSLLGDRVTIAAADGgvSLTQVGGWAHKLPSNPEDNIVHQCAVFFLKALGKE 81 
                                     68*********************************999999899*********************************** PP

                       TIGR00191  78 vkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlqlavke 150
                                       +v+lt+ek++p+g+GLGSSa+++vaa++a+ne++g +++k+ ll+l+++ Eg      H+DNvap++lGG+ql+++ 
  lcl|FitnessBrowser__MR1:202521  82 NRGVALTLEKNLPVGSGLGSSASSVVAALYALNEHFGCPYDKQALLELMGEFEGkisgsvHYDNVAPCYLGGMQLMLNV 160
                                     ******************************************************************************* PP

                       TIGR00191 151 ddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkDrvhqpy 229
                                        +++  +Ps++++++v+++P+i++sTa  R+++P++y+ + ++  ++ l+ +v+A +++ +a+l+  ++kD++++py
  lcl|FitnessBrowser__MR1:202521 161 PG-AICEAIPSFKQWYWVVAYPGISLSTAMMRKLMPEQYDKSVVIDFGRYLSAFVHASYQQ-NAQLAIQVLKDVLAEPY 237
                                     99.**********************************************************.***************** PP

                       TIGR00191 230 RekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakegieltvkvleldtdgae 300
                                     R+  iP++++ + a +e g+l++++SG+Gpt+++++++   ++ a+ +le ++     ++ +v++ld +g++
  lcl|FitnessBrowser__MR1:202521 238 RAAAIPGYDNARAALAELGMLTTGISGSGPTLFSVTDDLAtANAAKAWLEANYLTDAGGFAHVCRLDEQGTR 309
                                     ***************************************99999*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (312 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: 11.20
//
[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