Alignments for a candidate for asp-kinase in Beijerinckia mobilis UQM 1969

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Beijerinckia mobilis UQM 1969

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_034993625.1 DL88_RS06715 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_000745425.1:WP_034993625.1
          Length = 411

 Score =  405 bits (1042), Expect = e-118
 Identities = 225/413 (54%), Positives = 285/413 (69%), Gaps = 8/413 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           M  +V KFGGTSV T++RI  VA  V + R+AG D+ VVVSAMSG+TN L+G   +    
Sbjct: 1   MPRLVMKFGGTSVATIDRIRNVARHVIRERKAGYDIAVVVSAMSGKTNELVGWCQEAASF 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
             P E D +V++GEQVT  LL++ L   G+PA S+ G QV ILT  AH  ARI  ID T+
Sbjct: 61  YDPAEYDAVVASGEQVTAGLLAIVLRDLGLPARSWQGWQVPILTSDAHASARITSIDGTN 120

Query: 121 -IRADLKAGRVVVVAGFQGVDG-NGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 178
            I    + G + VV GFQG+    G ITTLGRGGSDT+ VA+AAA+ A+ C IYTDVDGV
Sbjct: 121 LINGFSERGEIAVVTGFQGIHAPTGRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGV 180

Query: 179 YTTDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEG--- 235
           YTTDPRVVP+ARRLDKI FEEMLEMASLG+KVLQ+R+VE A  + V   V  SF +    
Sbjct: 181 YTTDPRVVPKARRLDKIAFEEMLEMASLGAKVLQVRSVELAMLHRVKTFVRSSFDDPESP 240

Query: 236 -PGTLITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDM 294
            PGTLI   DEE+ +EQ +++GIAF RDEA++T+R V D PGVA  I  P++ AN+ VDM
Sbjct: 241 KPGTLIC--DEEDIVEQQVVTGIAFQRDEAQITLRRVADHPGVAAAIFVPLAEANINVDM 298

Query: 295 IVQNVAHDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSH 354
           I+Q  + D+ TD TFTV   D+  A ++L +    IG     G  ++ KVS +GVGMRSH
Sbjct: 299 IIQVASDDHATDITFTVPGTDFERAKQVLTKAQPQIGFTNLQGTADMVKVSAIGVGMRSH 358

Query: 355 AGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 407
           AGVA+R F+AL+ + INI+ I+TSEIK S++IE  Y ELAVR LHT + LD P
Sbjct: 359 AGVAARAFKALSDKGINIRAITTSEIKFSILIEAPYTELAVRTLHTLYGLDQP 411


Lambda     K      H
   0.317    0.133    0.362 

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: 422
Number of extensions: 15
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: 412
Length of database: 411
Length adjustment: 31
Effective length of query: 381
Effective length of database: 380
Effective search space:   144780
Effective search space used:   144780
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_034993625.1 DL88_RS06715 (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.3231443.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-127  410.2   2.4   5.5e-127  410.1   2.4    1.0  1  NCBI__GCF_000745425.1:WP_034993625.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745425.1:WP_034993625.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.1   2.4  5.5e-127  5.5e-127       4     404 ..       4     406 ..       1     409 [. 0.95

  Alignments for each domain:
  == domain 1  score: 410.1 bits;  conditional E-value: 5.5e-127
                             TIGR00656   4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelv 76 
                                            V+KFGGtsv+ ++ri+++a++v++e k g++  VVvSAms++t+elv         +   +   p+e d +v
  NCBI__GCF_000745425.1:WP_034993625.1   4 LVMKFGGTSVATIDRIRNVARHVIRERKAGYDIAVVVSAMSGKTNELVGWC------QEAASFYDPAEYDAVV 70 
                                           69*************************************************......57778899******** PP

                             TIGR00656  77 svGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat.e 148
                                           + GE++++ ll+ +lr+lg  a++ +g++ +ilT+d + +A+i++++  + +    e+g i vv+GF+G    
  NCBI__GCF_000745425.1:WP_034993625.1  71 ASGEQVTAGLLAIVLRDLGLPARSWQGWQVPILTSDAHASARITSIDGTNLINGFSERGEIAVVTGFQGIHaP 143
                                           ************************************************7777778899***********7627 PP

                             TIGR00656 149 eGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpr 221
                                            G+iTtLGRGGSD++A+++aaa+ A+r++iyTDV+GvyttDPrvv++a+++dki++eE+le+A+lGakvl+ r
  NCBI__GCF_000745425.1:WP_034993625.1 144 TGRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVYTTDPRVVPKARRLDKIAFEEMLEMASLGAKVLQVR 216
                                           9************************************************************************ PP

                             TIGR00656 222 alelaveakvpilvrsske....keegTlitn..kkensslvkaialeknvarltvegegmlgkrgilaeifk 288
                                           ++ela+   v+ +vrss++    ++ gTli++  +  ++++v++ia++++ a++t++   +++++g++a if 
  NCBI__GCF_000745425.1:WP_034993625.1 217 SVELAMLHRVKTFVRSSFDdpesPKPGTLICDeeDIVEQQVVTGIAFQRDEAQITLR--RVADHPGVAAAIFV 287
                                           *****************973322458*****966555668*****************..************** PP

                             TIGR00656 289 aLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapG 358
                                            Lae++invd+i+q  s+   t+i+++v  +d ++ak++L++ + ++++++l+   d+ +vs++g+g++++ G
  NCBI__GCF_000745425.1:WP_034993625.1 288 PLAEANINVDMIIQVASDdhaTDITFTVPGTDFERAKQVLTKAQPQIGFTNLQGTADMVKVSAIGVGMRSHAG 360
                                           ***************999999**************************************************** PP

                             TIGR00656 359 vaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404
                                           va+++fkal++k+ini  i++se+k s+l++  ++e avr+lh  +
  NCBI__GCF_000745425.1:WP_034993625.1 361 VAARAFKALSDKGINIRAITTSEIKFSILIEAPYTELAVRTLHTLY 406
                                           *******************************************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (411 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: 28.43
//
[ok]

This GapMind analysis is from Jul 25 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:

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