GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Cupriavidus basilensis 4G11

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate RR42_RS06370 RR42_RS06370 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__Cup4G11:RR42_RS06370
          Length = 416

 Score =  519 bits (1336), Expect = e-152
 Identities = 276/416 (66%), Positives = 328/416 (78%), Gaps = 12/416 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIV K+GGTS+GS ERI+ VA +V K+  AG  +VVV SAMSGETNRL+ LAK IS  
Sbjct: 1   MALIVHKYGGTSMGSPERIKNVAKRVAKWHRAGHRVVVVPSAMSGETNRLLGLAKEISA- 59

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP PRELD++ +TGEQ + ALLA+AL   GV A+SYTG QV + TDS+HTKARI  IDD
Sbjct: 60  -QPSPRELDMLAATGEQASSALLAIALQSEGVDAISYTGWQVPVKTDSSHTKARIESIDD 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           ++I  DL AGRVVVV GFQG+D+ GNITTLGRGGSDT+ VA+AAA++A+EC IYTDVDGV
Sbjct: 119 ERILADLDAGRVVVVTGFQGIDDNGNITTLGRGGSDTSAVAIAAAIEAEECLIYTDVDGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE---- 236
           YTTDPRVV  A+RLD+ITFEEMLEMASLGSKVLQIR+VEFAGKY V  RVL S  +    
Sbjct: 179 YTTDPRVVEDARRLDQITFEEMLEMASLGSKVLQIRSVEFAGKYRVKTRVLSSLTDPLMP 238

Query: 237 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANI 291
                  GTLIT +E   ME  +ISGIAF RDEAK+T+ GVPD PG+A++ILGP++ ANI
Sbjct: 239 LEQEMHSGTLITFEENSEMEAAVISGIAFARDEAKITVLGVPDKPGIAYQILGPVADANI 298

Query: 292 EVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGV 350
           +VDMI+QN S D  TDFTFTV R EY  A  IL ++ K  IGA  V GD K++KVS+VGV
Sbjct: 299 DVDMIIQNQSVDGKTDFTFTVPRGEYQRALAILNDSVKAHIGAASVSGDPKVSKVSVVGV 358

Query: 351 GMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406
           GMRSH G+AS+MF  L++E INIQMISTSEIK+SV+I+EKY+ELAVRALH  FELD
Sbjct: 359 GMRSHVGIASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKVFELD 414


Lambda     K      H
   0.316    0.133    0.357 

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: 517
Number of extensions: 19
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: 413
Length of database: 416
Length adjustment: 31
Effective length of query: 382
Effective length of database: 385
Effective search space:   147070
Effective search space used:   147070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate RR42_RS06370 RR42_RS06370 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (EC 2.7.2.4))

# 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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.23855.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-130  421.1   7.5   2.8e-130  420.9   7.5    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS06370  RR42_RS06370 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS06370  RR42_RS06370 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.9   7.5  2.8e-130  2.8e-130       1     406 [.       1     413 [.       1     414 [. 0.95

  Alignments for each domain:
  == domain 1  score: 420.9 bits;  conditional E-value: 2.8e-130
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liV K+GGts+gs erik++ak+v k  + g++vvVV SAms++t++l+ la      + is ++sp
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370   1 MALIVHKYGGTSMGSPERIKNVAKRVAKWHRAGHRVVVVPSAMSGETNRLLGLA------KEISAQPSP 63 
                                               579***************************************************......9******** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d+l ++GE+ ssall+ al+ +gv+a++++g++ ++ Td+++++A+i++++  er+l  L+ g +v
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370  64 RELDMLAATGEQASSALLAIALQSEGVDAISYTGWQVPVKTDSSHTKARIESIDD-ERILADLDAGRVV 131
                                               ******************************************************9.************* PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               vv+GF+G + +G+iTtLGRGGSD++A+++aaa++A+++ iyTDV+GvyttDPrvve+a+++d+i++eE+
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370 132 VVTGFQGIDDNGNITTLGRGGSDTSAVAIAAAIEAEECLIYTDVDGVYTTDPRVVEDARRLDQITFEEM 200
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrss.........kekeegTlitn..kkens.slvkaialek 264
                                               le+A+lG kvl+ r++e+a ++ v+ +v ss         +e ++gTlit   ++e++  ++++ia+ +
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370 201 LEMASLGSKVLQIRSVEFAGKYRVKTRVLSSltdplmpleQEMHSGTLITFeeNSEMEaAVISGIAFAR 269
                                               ****************************99844444433234459****97563344356********* PP

                                 TIGR00656 265 nvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesg 330
                                               + a++tv   g+ +k+gi+ +i + +a+++i+vd+i+q +s    t+ +++v + + ++a ++L++ ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370 270 DEAKITVL--GVPDKPGIAYQILGPVADANIDVDMIIQNQSVdgkTDFTFTVPRGEYQRALAILNDSVK 336
                                               ********..9****************************987777********************9986 PP

                                 TIGR00656 331 a.aelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavr 398
                                               a ++  s++ + ++ +vs+vg+g++++ G+as++f  l+e++ini mis+se+kisvl+dek++e avr
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370 337 AhIGAASVSGDPKVSKVSVVGVGMRSHVGIASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVR 405
                                               61469**************************************************************** PP

                                 TIGR00656 399 klheklee 406
                                               +lh+++e+
  lcl|FitnessBrowser__Cup4G11:RR42_RS06370 406 ALHKVFEL 413
                                               ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (416 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.03
//
[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:

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