Alignments for a candidate for thrB in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Shewanella amazonensis SB2B

Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate 6936719 Sama_0906 homoserine kinase (RefSeq)

Query= CharProtDB::CH_002113
         (310 letters)



>FitnessBrowser__SB2B:6936719
          Length = 314

 Score =  348 bits (892), Expect = e-100
 Identities = 172/307 (56%), Positives = 226/307 (73%), Gaps = 3/307 (0%)

Query: 4   VYAPASSANMSVGFDVLGAAVTPVDGALLGD-VVTVEAAETFSLNNLGRFADKLPSEPRE 62
           VYAPAS  N+ VGFD+LGAA+ P++G+LLGD V+  EA    +LN  G +A KLP+ PRE
Sbjct: 5   VYAPASMGNVGVGFDLLGAALAPIEGSLLGDRVMIAEANAGLTLNTTGAWAHKLPANPRE 64

Query: 63  NIVYQCWERFCQELGKQ-IPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDT 121
           NIV+QC E F Q LGK+ + +A+TLEKN+P+GSGLGSSA SVVAAL A+NE+  KP ++ 
Sbjct: 65  NIVWQCAEFFLQRLGKEELGIALTLEKNLPVGSGLGSSASSVVAALYALNEYFDKPFDEQ 124

Query: 122 RLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIK 181
            LLALMGE EG+ISGS+HYDNVAPC+LGGMQLM++    I + +P F+ W WV+AYPGI 
Sbjct: 125 ALLALMGEFEGKISGSVHYDNVAPCYLGGMQLMLDLPGRICESIPSFEHWYWVVAYPGIS 184

Query: 182 VSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPG 241
           +STA+ RA++P  Y +   I  GRHL+ F+HA Y +   LA  ++KDV+AEPYR   +PG
Sbjct: 185 LSTAKMRALMPDSYDKSVVIDFGRHLSAFVHASYRQDEALALAVLKDVLAEPYRAPAIPG 244

Query: 242 FRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLD 301
           + +AR A+AE+G + SGISGSGPTLF++    ETA+    WL  +YL  + GF H+CRLD
Sbjct: 245 YLEARDALAELGMLTSGISGSGPTLFSVTSCLETAEAAKAWLEAHYL-TEGGFAHVCRLD 303

Query: 302 TAGARVL 308
             G RV+
Sbjct: 304 MQGTRVV 310


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: 314
Number of extensions: 13
Number of successful extensions: 4
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: 314
Length adjustment: 27
Effective length of query: 283
Effective length of database: 287
Effective search space:    81221
Effective search space used:    81221
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 6936719 Sama_0906 (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.25636.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.6e-88  281.3   0.0    4.1e-88  281.1   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6936719  Sama_0906 homoserine kinase (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936719  Sama_0906 homoserine kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.1   0.0   4.1e-88   4.1e-88       1     302 [.       3     310 ..       3     312 .. 0.96

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 4.1e-88
                         TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk..sleaegegvekipkesdkNliyqvakkvlkklg 75 
                                       l+v++Pas  N+g+GfD lG+al +++++l+++ v ++++++   l+++g  ++k+p+++++N++ q+a+ +l++lg
  lcl|FitnessBrowser__SB2B:6936719   3 LTVYAPASMGNVGVGFDLLGAALAPIEGSLLGDRVMIAEANAglTLNTTGAWAHKLPANPRENIVWQCAEFFLQRLG 79 
                                       68*******************************99777777767899999999************************ PP

                         TIGR00191  76 krvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlql 146
                                       k+  +++lt+ek++p+g+GLGSSa+++vaa++a+ne ++++++++ ll+l+++ Eg      H+DNvap++lGG+ql
  lcl|FitnessBrowser__SB2B:6936719  80 KEELGIALTLEKNLPVGSGLGSSASSVVAALYALNEYFDKPFDEQALLALMGEFEGkisgsvHYDNVAPCYLGGMQL 156
                                       ***************************************************************************** PP

                         TIGR00191 147 avkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkD 223
                                       ++      ++ ++Ps++++++v+++P+i++sTa+ Ra++P +y+ + ++  ++hl+ +v+A + +  + l+  ++kD
  lcl|FitnessBrowser__SB2B:6936719 157 MLDLPG-RICESIPSFEHWYWVVAYPGISLSTAKMRALMPDSYDKSVVIDFGRHLSAFVHASYRQ-DEALALAVLKD 231
                                       **9999.9*********************************************************.778888999** PP

                         TIGR00191 224 rvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakegieltvkvleldtdga 299
                                       ++++pyR+  iP++ e + a +e g+l++++SG+Gpt++++++  + +e a+ +le ++   + ++ +v++ld++g+
  lcl|FitnessBrowser__SB2B:6936719 232 VLAEPYRAPAIPGYLEARDALAELGMLTSGISGSGPTLFSVTSCLEtAEAAKAWLEAHYLT-EGGFAHVCRLDMQGT 307
                                       *******************************************999888999999988875.67899********** PP

                         TIGR00191 300 eve 302
                                       +v+
  lcl|FitnessBrowser__SB2B:6936719 308 RVV 310
                                       997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (314 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: 8.44
//
[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