Alignments for a candidate for thrB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Herbaspirillum seropedicae SmR1

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate HSERO_RS02240 HSERO_RS02240 homoserine kinase

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__HerbieS:HSERO_RS02240
          Length = 318

 Score =  230 bits (586), Expect = 4e-65
 Identities = 130/304 (42%), Positives = 177/304 (58%), Gaps = 6/304 (1%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           M+VFTP+    L  +L  + LG     +GI+ G ENSNFF+  E GE+VLTL E+  ++ 
Sbjct: 1   MAVFTPVSLEQLSDWLKHFPLGTATSIKGISSGIENSNFFIGTERGEYVLTLFEKLHIEQ 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           LPF++EL+  L E G+PVP  +    G  +  L  KPA +  +L G+ +  P   HC  +
Sbjct: 61  LPFYLELMRHLAERGIPVPAPVANDKGAIVSLLNDKPAAIVSKLEGQSQLDPQPVHCAAL 120

Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPAL--AEIAALDA 178
           GD+L  +H A +   + +P+ RGL W LE    + P LP +   LLA  +   +  A  A
Sbjct: 121 GDMLARMHLAAKDFKILQPNLRGLAWWLETTPTVLPFLPAELGRLLADEVQYQKDFAATA 180

Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNA-CSGWMLYDLAITLNDWCSNTD-GS 236
           +  ALPR  +HADLFR+N +F G  L+G+ DFY A C  W L+DLA+T+NDWC + D G 
Sbjct: 181 DYRALPRGPVHADLFRNNAMFVGERLSGIFDFYFAGCDTW-LFDLAVTVNDWCVDLDTGV 239

Query: 237 LDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLI-HDP 295
           LD AR  A+LAAY   RPF+  E   W  MLR A +RFWLSRL         ++L  HDP
Sbjct: 240 LDLARTEAMLAAYRAVRPFSEAERIAWQPMLRAAALRFWLSRLYDFYMPRAAEMLTPHDP 299

Query: 296 AEFE 299
             FE
Sbjct: 300 THFE 303


Lambda     K      H
   0.324    0.140    0.434 

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: 10
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: 316
Length of database: 318
Length adjustment: 27
Effective length of query: 289
Effective length of database: 291
Effective search space:    84099
Effective search space used:    84099
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate HSERO_RS02240 HSERO_RS02240 (homoserine kinase)
to HMM TIGR00938 (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/TIGR00938.hmm
# target sequence database:        /tmp/gapView.1059.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00938  [M=307]
Accession:   TIGR00938
Description: thrB_alt: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.2e-106  341.6   0.0   2.5e-106  341.4   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS02240  HSERO_RS02240 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS02240  HSERO_RS02240 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.4   0.0  2.5e-106  2.5e-106       1     306 [.       1     307 [.       1     308 [. 0.97

  Alignments for each domain:
  == domain 1  score: 341.4 bits;  conditional E-value: 2.5e-106
                                  TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflel 68 
                                                mav+t vs e+l+ +L+ + lG   s+kGi++G+ensn+++ t++g yvLtl+ek    e+LPf+lel
  lcl|FitnessBrowser__HerbieS:HSERO_RS02240   1 MAVFTPVSLEQLSDWLKHFPLGTATSIKGISSGIENSNFFIGTERGEYVLTLFEKLH-IEQLPFYLEL 67 
                                                9******************************************************99.9********* PP

                                  TIGR00938  69 lthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfk 136
                                                ++hLaerg+pv++pv++ +G+ +s L+ kPaa+v+ L+G+s   P++ +c++ g++la++hla++dfk
  lcl|FitnessBrowser__HerbieS:HSERO_RS02240  68 MRHLAERGIPVPAPVANDKGAIVSLLNDKPAAIVSKLEGQSQLDPQPVHCAALGDMLARMHLAAKDFK 135
                                                ******************************************************************** PP

                                  TIGR00938 137 eerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp....rdLPrgvihadlfkdnvl 200
                                                  + n lr  aW+ +++ +  vl++l +el++ll +e+++ k+f +    r LPrg +hadlf++n +
  lcl|FitnessBrowser__HerbieS:HSERO_RS02240 136 ILQPN-LRGLAWWLETTPT--VLPFLPAELGRLLADEVQYQKDFAAtadyRALPRGPVHADLFRNNAM 200
                                                *****.***********99..*****************99998864333389**************** PP

                                  TIGR00938 201 ldgdklkgvidfyfaCedallydlaiavndWcfeadd.kldaaaakallkgyeavrpLseeekaafpv 267
                                                + g++l+g+ dfyfa  d++l+dla++vndWc++ d+  ld a++ a+l +y+avrp+se e+ a+  
  lcl|FitnessBrowser__HerbieS:HSERO_RS02240 201 FVGERLSGIFDFYFAGCDTWLFDLAVTVNDWCVDLDTgVLDLARTEAMLAAYRAVRPFSEAERIAWQP 268
                                                **********************************99636899************************** PP

                                  TIGR00938 268 llrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306
                                                +lr+aalrf+lsrl d+++++a e+ ++ dP++fer+L+
  lcl|FitnessBrowser__HerbieS:HSERO_RS02240 269 MLRAAALRFWLSRLYDFYMPRAAEMLTPHDPTHFERILR 307
                                                *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (318 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.74
//
[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