Alignments for a candidate for thrB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Pseudomonas simiae WCS417

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate GFF78 PS417_00395 serine kinase

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__WCS417:GFF78
          Length = 317

 Score =  459 bits (1180), Expect = e-134
 Identities = 231/317 (72%), Positives = 260/317 (82%), Gaps = 1/317 (0%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           MSVFTPL R  LE FLAPY LGRL DF+GIA GSEN+NFF+SLE GEFVLTLVERGPV +
Sbjct: 1   MSVFTPLARPELETFLAPYGLGRLIDFQGIAAGSENTNFFISLEQGEFVLTLVERGPVAE 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           +PFFIELLDVLH+  LPVPYALRT DG ALR L+GKPALLQPRLAG+H ++ NA HC +V
Sbjct: 61  MPFFIELLDVLHDADLPVPYALRTTDGVALRELKGKPALLQPRLAGKHIKEANAQHCAQV 120

Query: 121 GDLLGHLHAATRG-RILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAE 179
           G+LLGHLH AT+G ++LER +DRGL WML +GA L   L +  + LL  AL+EI A  A 
Sbjct: 121 GELLGHLHLATQGEKVLERKTDRGLDWMLSEGAQLISHLNDAQQRLLQDALSEIEAHKAG 180

Query: 180 RPALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDP 239
             ALPRAN+HADLFRDN +F+G HL GLIDFYNACSG MLYD+AI LNDWCS+ DG +D 
Sbjct: 181 ILALPRANVHADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALNDWCSDADGVIDG 240

Query: 240 ARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFE 299
            RARALL AYA+ RPFTA EAE WP+MLRVACVRFWLSRLIAAE+FAGQDVLIHDPAEFE
Sbjct: 241 QRARALLGAYASLRPFTAKEAELWPTMLRVACVRFWLSRLIAAESFAGQDVLIHDPAEFE 300

Query: 300 IRLAQRQNVEIHLPFAL 316
            RL QRQ V I LPFAL
Sbjct: 301 HRLVQRQQVTIQLPFAL 317


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: 381
Number of extensions: 8
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: 316
Length of database: 317
Length adjustment: 27
Effective length of query: 289
Effective length of database: 290
Effective search space:    83810
Effective search space used:    83810
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 GFF78 PS417_00395 (serine 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.5109.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.2e-87  280.0   0.0    1.4e-87  279.9   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF78  PS417_00395 serine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF78  PS417_00395 serine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.9   0.0   1.4e-87   1.4e-87       1     305 [.       1     303 [.       1     305 [. 0.94

  Alignments for each domain:
  == domain 1  score: 279.9 bits;  conditional E-value: 1.4e-87
                         TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellthLaergl 77 
                                       m+v+t ++  ele+fL  y lG+l++++Gia G en+n+++  ++g +vLtl e+     e+Pff+ell+ L + +l
  lcl|FitnessBrowser__WCS417:GFF78   1 MSVFTPLARPELETFLAPYGLGRLIDFQGIAAGSENTNFFISLEQGEFVLTLVERGP-VAEMPFFIELLDVLHDADL 76 
                                       9*****************************************************998.889**************** PP

                         TIGR00938  78 pvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerkndlrleaWsilaak 154
                                       pv+ ++++ dG al eL+GkPa l   L+G+ +++  a++c++vge l +lhla+++ k   +   r  +W     +
  lcl|FitnessBrowser__WCS417:GFF78  77 PVPYALRTTDGVALRELKGKPALLQPRLAGKHIKEANAQHCAQVGELLGHLHLATQGEKVLERKTDRGLDWMLSEGA 153
                                       ******************************************************9776654444478999*999998 PP

                         TIGR00938 155 kfkvleqleeelaalldkeldalkkflp..rdLPrgvihadlfkdnvlldgdklkgvidfyfaCedallydlaiavn 229
                                       +  ++ +l++ +++ll++ l  ++   +    LPr+ +hadlf+dn +++g +l+g+idfy aC++ +lyd+aia+n
  lcl|FitnessBrowser__WCS417:GFF78 154 Q--LISHLNDAQQRLLQDALSEIEAHKAgiLALPRANVHADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALN 228
                                       8..999**********99998887666522589******************************************** PP

                         TIGR00938 230 dWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkL 305
                                       dWc +ad+ +d ++a+all++y + rp++++e + +p++lr+a++rf+lsrl     + ag+ v + dPaefe++L
  lcl|FitnessBrowser__WCS417:GFF78 229 DWCSDADGVIDGQRARALLGAYASLRPFTAKEAELWPTMLRVACVRFWLSRLIAAE-SFAGQDVLIHDPAEFEHRL 303
                                       ****************************************************9865.57899999********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (317 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: 10.76
//
[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