GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Phyllobacterium endophyticum PEPV15

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_106718999.1 CU100_RS23075 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_003010935.1:WP_106718999.1
          Length = 417

 Score =  404 bits (1039), Expect = e-117
 Identities = 220/416 (52%), Positives = 291/416 (69%), Gaps = 13/416 (3%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MA IV KFGGTSV  I+RI  VA  VK+  +AG ++ VV+SAM+G+TN L+   +Q +  
Sbjct: 1   MARIVMKFGGTSVADIDRIRNVARHVKREVDAGHEVAVVVSAMAGKTNELVAWTRQTSPM 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
              RE D IV++GEQVT  LL +AL   GV A S+ G Q+ I TD++H  ARIL ID   
Sbjct: 61  HDAREYDAIVASGEQVTAGLLAIALQAMGVHARSWQGWQIPIKTDNAHGAARILDIDGSF 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +     EG+V V++GFQG+     I+TLGRGGSDT+ VA+AA++KAD C IYTDVDGVYT
Sbjct: 121 LIERFAEGQVAVISGFQGIGPDNRISTLGRGGSDTSAVAIAASVKADRCDIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKE------ 234
           TDPRV P+ARRL +I+FEEMLEMASLG+KVLQ+RSVE A  + V   V  SF++      
Sbjct: 181 TDPRVEPKARRLSRISFEEMLEMASLGAKVLQVRSVELAMVHKVRTFVRSSFEDPDAPGM 240

Query: 235 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNI 289
                 PGTLI  DEEE +EQ +++GIA+ +DEA++++R V D PG++  I GP++ S+I
Sbjct: 241 GDLINPPGTLI-CDEEEIVEQQVVTGIAYAKDEAQISLRRVADRPGISAAIFGPLAESHI 299

Query: 290 EVDMIVQNVAHDNT-TDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGV 348
            VDMIVQNV+ D T TD TFTV   + +KA  VLEN   EIG   +  +  + KVS++G+
Sbjct: 300 NVDMIVQNVSEDGTKTDMTFTVPSGDLDKALVVLENVKAEIGCDIIQSEAGMVKVSVIGI 359

Query: 349 GMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           GMRSHAGVA+  F ALA + INI+ I+TSEIK+S++++  Y ELAVR LH+ + LD
Sbjct: 360 GMRSHAGVAATAFRALADKGINIRAITTSEIKISILIDGPYAELAVRTLHSVYGLD 415


Lambda     K      H
   0.316    0.133    0.358 

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: 425
Number of extensions: 14
Number of successful extensions: 3
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: 411
Length of database: 417
Length adjustment: 31
Effective length of query: 380
Effective length of database: 386
Effective search space:   146680
Effective search space used:   146680
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 WP_106718999.1 CU100_RS23075 (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.525945.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-126  406.9   6.4     6e-126  406.6   6.4    1.1  1  NCBI__GCF_003010935.1:WP_106718999.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106718999.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.6   6.4    6e-126    6e-126       3     405 ..       3     413 ..       1     415 [. 0.95

  Alignments for each domain:
  == domain 1  score: 406.6 bits;  conditional E-value: 6e-126
                             TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                            iV+KFGGtsv++++ri+++a++v++e+  g++v VVvSAm+++t+elv+ +      +++s     re d +
  NCBI__GCF_003010935.1:WP_106718999.1   3 RIVMKFGGTSVADIDRIRNVARHVKREVDAGHEVAVVVSAMAGKTNELVAWT------RQTSPMHDAREYDAI 69 
                                           59**************************************************......788999999****** PP

                             TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGate 148
                                           v+ GE++++ ll+ al++ gv+a++ +g++ +i Td+ +g A+i +++  + L+e+ +eg++ v+ GF+G   
  NCBI__GCF_003010935.1:WP_106718999.1  70 VASGEQVTAGLLAIALQAMGVHARSWQGWQIPIKTDNAHGAARILDIDG-SFLIERFAEGQVAVISGFQGIGP 141
                                           *************************************************.*********************** PP

                             TIGR00656 149 eGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpr 221
                                           + +i tLGRGGSD++A+++aa++kAdr++iyTDV+GvyttDPrv ++a+++ +is+eE+le+A+lGakvl+ r
  NCBI__GCF_003010935.1:WP_106718999.1 142 DNRISTLGRGGSDTSAVAIAASVKADRCDIYTDVDGVYTTDPRVEPKARRLSRISFEEMLEMASLGAKVLQVR 214
                                           ************************************************************************* PP

                             TIGR00656 222 alelaveakvpilvrsskek..........e.egTlitn..kkensslvkaialeknvarltvegegmlgkrg 281
                                           ++ela+  kv  +vrss+e           +  gTli++  +  ++++v++ia+ k+ a+++++   +++++g
  NCBI__GCF_003010935.1:WP_106718999.1 215 SVELAMVHKVRTFVRSSFEDpdapgmgdliNpPGTLICDeeEIVEQQVVTGIAYAKDEAQISLR--RVADRPG 285
                                           *****************985333333322233688998844334458*****************..******* PP

                             TIGR00656 282 ilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivg 350
                                           i a if+ Lae++invd+i+q  se    t+++++v   d+d+a  +L++++ +++ + ++ e ++ +vs++g
  NCBI__GCF_003010935.1:WP_106718999.1 286 ISAAIFGPLAESHINVDMIVQNVSEdgtkTDMTFTVPSGDLDKALVVLENVKAEIGCDIIQSEAGMVKVSVIG 358
                                           ************************99999******************************************** PP

                             TIGR00656 351 aglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                            g++++ Gva+ +f al++k+ini  i++se+kis+l+d+ +ae avr+lh+++ 
  NCBI__GCF_003010935.1:WP_106718999.1 359 IGMRSHAGVAATAFRALADKGINIRAITTSEIKISILIDGPYAELAVRTLHSVYG 413
                                           ***************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (417 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: 30.65
//
[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