GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB in Novosphingobium barchaimii LL02

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_059149707.1 V474_RS00925 homoserine kinase

Query= reanno::Korea:Ga0059261_3253
         (319 letters)



>NCBI__GCF_001046635.1:WP_059149707.1
          Length = 334

 Score =  325 bits (833), Expect = 9e-94
 Identities = 177/321 (55%), Positives = 215/321 (66%), Gaps = 11/321 (3%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVET-----TRDRFILTLYEK 55
           MAVYT++ AE +A  ++ +DVG LVSAKGIAEGV NSN+L+ET     +  RFILT+YE 
Sbjct: 1   MAVYTRLGAEEMAVIISAFDVGTLVSAKGIAEGVSNSNWLIETQDAAGSARRFILTMYES 60

Query: 56  RVEAADLPYFMGLLDHLAAKGLPVPPAIKDRGGVEI---QELNGRPA-CLIKFLSGISLS 111
           R E A+LP+F+ LLDHLAAK  PVP  + D  G      Q   G  A  LI+FL G+S+S
Sbjct: 61  RTEVAELPFFLDLLDHLAAKHCPVPRTMHDSEGASHRLHQTPEGTKALALIEFLPGVSVS 120

Query: 112 HPTPAQARAAGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHS-LDQIVPGLYDDL 170
            PTPAQARA G A+AQ+H A ADFP  R NS+ +  WQ L   CG   L+ I P L   +
Sbjct: 121 EPTPAQARAVGGALAQIHLAAADFPASRTNSLALADWQQLLRDCGREGLESIHPELGHIV 180

Query: 171 GFAIARVVPAWTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHS 230
              +A +   W R D     IHADLFPDNVLM GD VTGLIDFYFACTD+  YD+AV H+
Sbjct: 181 ERELALLAARWPR-DLPSGVIHADLFPDNVLMLGDTVTGLIDFYFACTDLFAYDVAVTHA 239

Query: 231 AWSFDAHGRNYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTP 290
           AW F   G  + PA+ DAL+AGY A  PL+  E AA P LA GA +RF  +RA+DWLNTP
Sbjct: 240 AWCFSPDGTRFLPALSDALMAGYSAVRPLSPAEHAALPLLARGAAMRFLATRAYDWLNTP 299

Query: 291 ADALVMRKDPLAYVRRLKHYA 311
           ADALV  KDP+A+ RRL+ YA
Sbjct: 300 ADALVTPKDPMAFARRLEFYA 320


Lambda     K      H
   0.323    0.138    0.429 

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: 343
Number of extensions: 15
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: 319
Length of database: 334
Length adjustment: 28
Effective length of query: 291
Effective length of database: 306
Effective search space:    89046
Effective search space used:    89046
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_059149707.1 V474_RS00925 (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.3086301.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-110  355.6   0.0   1.4e-110  355.4   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059149707.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059149707.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.4   0.0  1.4e-110  1.4e-110       1     306 [.       1     317 [.       1     318 [. 0.95

  Alignments for each domain:
  == domain 1  score: 355.4 bits;  conditional E-value: 1.4e-110
                             TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttd.....kgryvLtlyekrvkaeeLPfflel 68 
                                           mavyt +  ee+   ++ +d+G l+s kGiaeGv nsn+l++t+      +r++Lt+ye r++  eLPffl+l
  NCBI__GCF_001046635.1:WP_059149707.1   1 MAVYTRLGAEEMAVIISAFDVGTLVSAKGIAEGVSNSNWLIETQdaagsARRFILTMYESRTEVAELPFFLDL 73 
                                           9******************************************73333358********************** PP

                             TIGR00938  69 lthLaerglpvakpvksrdG...ralseLaGkPa.alvefLkGssvakPtaercrevgevlaklhlagadfke 137
                                           l+hLa++  pv+++++  +G   r+ ++ +G  a al+efL+G sv++Pt++++r+vg  la++hla+adf++
  NCBI__GCF_001046635.1:WP_059149707.1  74 LDHLAAKHCPVPRTMHDSEGashRLHQTPEGTKAlALIEFLPGVSVSEPTPAQARAVGGALAQIHLAAADFPA 146
                                           *****************9993333457777855549************************************* PP

                             TIGR00938 138 erkndlrleaWsilaakk.fkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklkgv 209
                                           +r+n+l l++W+ l   + ++ le +++el++ +++el+ l   +prdLP+gvihadlf+dnvl+ gd ++g+
  NCBI__GCF_001046635.1:WP_059149707.1 147 SRTNSLALADWQQLLRDCgREGLESIHPELGHIVERELALLAARWPRDLPSGVIHADLFPDNVLMLGDTVTGL 219
                                           ******************99***************************************************** PP

                             TIGR00938 210 idfyfaCedallydlaiavndWcfeadd.kldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrl 281
                                           idfyfaC+d ++yd+a++  +Wcf  d+ ++  a   al+ gy avrpLs+ e+aa+p l+rgaa+rfl +r+
  NCBI__GCF_001046635.1:WP_059149707.1 220 IDFYFACTDLFAYDVAVTHAAWCFSPDGtRFLPALSDALMAGYSAVRPLSPAEHAALPLLARGAAMRFLATRA 292
                                           *************************9962699***************************************** PP

                             TIGR00938 282 ldlvftqagelvvakdPaeferkLk 306
                                            d+ +t+a++lv++kdP +f r+L+
  NCBI__GCF_001046635.1:WP_059149707.1 293 YDWLNTPADALVTPKDPMAFARRLE 317
                                           ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (334 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: 15.72
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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