GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asp-kinase in Magnetospirillum magneticum AMB-1

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011384021.1 AMB_RS08140 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384021.1 AMB_RS08140 aspartate
           kinase
          Length = 406

 Score =  437 bits (1125), Expect = e-127
 Identities = 233/410 (56%), Positives = 307/410 (74%), Gaps = 8/410 (1%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MA IV KFGGTSV  +ERI+ VA++VK+  DAG+ + VV+SAMSG TN+L+     ++  
Sbjct: 1   MARIVMKFGGTSVADIERIKNVANRVKREFDAGNQVAVVVSAMSGATNQLVAWCNQVA-- 58

Query: 61  QQPL--PRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQI 118
             PL   RE D +V+TGEQVT  LLA+AL + GV A S+ G Q+ I TD  H KARI+ I
Sbjct: 59  --PLHDAREYDAVVATGEQVTTGLLAIALQELGVNARSWCGWQLPIRTDGVHGKARIMSI 116

Query: 119 DDQKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVD 178
           +  ++   +  G V VVAGFQG+     I TLGRGGSDT+ VALAAAL AD C IYTDVD
Sbjct: 117 ETDEMIARMGKGEVAVVAGFQGLGPDNRIATLGRGGSDTSAVALAAALHADRCDIYTDVD 176

Query: 179 GVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGP 238
           GVYTTDPR+VSVA++LDKIT+EEMLE+AS+G+KVLQ R+VE A K+ V ++VL SF++ P
Sbjct: 177 GVYTTDPRIVSVAKKLDKITYEEMLELASVGAKVLQTRSVEMAMKHRVRVQVLSSFEDKP 236

Query: 239 GTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQ 298
           GTL+  DE+E +E+ ++SGIA++RDEAK+T+  V D PGVA  I GP++ A + VDMIVQ
Sbjct: 237 GTLV-CDEDEIVEKELVSGIAYSRDEAKITLVRVADRPGVAASIFGPLAEAAVNVDMIVQ 295

Query: 299 NVSHD-NTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAG 357
           NVS D  +TD TFTV   + + A+++L++    +G  +++ D  + KVS++GVGMRSHAG
Sbjct: 296 NVSEDGKSTDLTFTVGNADLERAKKVLEDAKGNLGFEKLLADPNVVKVSVIGVGMRSHAG 355

Query: 358 VASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 407
           +A +MF+ LA E INIQ+ISTSEIK+SV+IEEKY ELA+RALHTA+ LDA
Sbjct: 356 IAQKMFQTLASEGINIQVISTSEIKISVLIEEKYTELALRALHTAYGLDA 405


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: 452
Number of extensions: 14
Number of successful extensions: 5
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: 406
Length adjustment: 31
Effective length of query: 382
Effective length of database: 375
Effective search space:   143250
Effective search space used:   143250
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_011384021.1 AMB_RS08140 (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.23098.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-135  436.3  10.9   6.8e-135  436.1  10.9    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384021.1  AMB_RS08140 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384021.1  AMB_RS08140 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.1  10.9  6.8e-135  6.8e-135       3     405 ..       3     402 ..       1     404 [. 0.97

  Alignments for each domain:
  == domain 1  score: 436.1 bits;  conditional E-value: 6.8e-135
                                 TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispre 71 
                                                iV+KFGGtsv+++erik++a++v++e   g++v VVvSAms+ t++lv+        +++      re
  lcl|NCBI__GCF_000009985.1:WP_011384021.1   3 RIVMKFGGTSVADIERIKNVANRVKREFDAGNQVAVVVSAMSGATNQLVAWC------NQVAPLHDARE 65 
                                               59**************************************************......788888899** PP

                                 TIGR00656  72 rdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvv 140
                                                d +v++GE++++ ll+ al+elgv+a++  g++ +i+Td+ +g+A+i +++t  +++ ++ +g + vv
  lcl|NCBI__GCF_000009985.1:WP_011384021.1  66 YDAVVATGEQVTTGLLAIALQELGVNARSWCGWQLPIRTDGVHGKARIMSIET-DEMIARMGKGEVAVV 133
                                               *****************************************************.8999999******** PP

                                 TIGR00656 141 aGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209
                                               aGF+G   + +i tLGRGGSD++A++laaal+Adr++iyTDV+GvyttDPr+v+ akk+dki+yeE+le
  lcl|NCBI__GCF_000009985.1:WP_011384021.1 134 AGFQGLGPDNRIATLGRGGSDTSAVALAAALHADRCDIYTDVDGVYTTDPRIVSVAKKLDKITYEEMLE 202
                                               ********************************************************************* PP

                                 TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegegm 276
                                               lA++Gakvl+ r++e+a++  v + v ss+e + gTl+++  +  +++lv++ia++++ a++t++   +
  lcl|NCBI__GCF_000009985.1:WP_011384021.1 203 LASVGAKVLQTRSVEMAMKHRVRVQVLSSFEDKPGTLVCDedEIVEKELVSGIAYSRDEAKITLV--RV 269
                                               ****************************************55455669*****************..** PP

                                 TIGR00656 277 lgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaeleslevee 341
                                               ++++g++a if+ Lae+ +nvd+i+q  se    t+++++v + d+++akk+L++ +g++++e+l  + 
  lcl|NCBI__GCF_000009985.1:WP_011384021.1 270 ADRPGVAASIFGPLAEAAVNVDMIVQNVSEdgksTDLTFTVGNADLERAKKVLEDAKGNLGFEKLLADP 338
                                               *****************************9999************************************ PP

                                 TIGR00656 342 dlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                               ++ +vs++g+g++++ G+a+++f+ l+ ++ini  is+se+kisvl++ek++e a r+lh ++ 
  lcl|NCBI__GCF_000009985.1:WP_011384021.1 339 NVVKVSVIGVGMRSHAGIAQKMFQTLASEGINIQVISTSEIKISVLIEEKYTELALRALHTAYG 402
                                               ************************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (406 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: 6.75
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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