Alignments for a candidate for asp-kinase in Methylohalobius crimeensis 10Ki

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methylohalobius crimeensis 10Ki

Align Aspartokinase 3; Aspartate kinase 3; Aspartokinase III; EC 2.7.2.4 (characterized)
to candidate WP_022948116.1 H035_RS0106110 aspartate kinase

Query= SwissProt::P94417
         (454 letters)



>NCBI__GCF_000421465.1:WP_022948116.1
          Length = 455

 Score =  285 bits (729), Expect = 2e-81
 Identities = 169/456 (37%), Positives = 263/456 (57%), Gaps = 16/456 (3%)

Query: 3   VVKFGGSSLASGAQLDKVFHIVTSDPARKAVVVSAPGKHYAEDTKVTDLLIACA------ 56
           V KFGGSS+AS  Q++KV  IV +D  R+ VVVSAPG+  +++ KVTD LI  A      
Sbjct: 6   VCKFGGSSVASAGQIEKVKQIVQADKRRRYVVVSAPGRSRSDEQKVTDHLINIATSGAHF 65

Query: 57  -EQYLATGSAPELAEAVVERYALIANELQLGQS-IIEKIRDDLFTLLEGDKSNPEQYLDA 114
            +Q L+  +  E  +AV+E++  IA+EL +    I+  ++ DL T LEGD+      +  
Sbjct: 66  RDQRLSI-TPNESKKAVLEKFTRIASELGVDAGDILASLKKDLATSLEGDRR-----IAF 119

Query: 115 VKASGEDNNAKLIAAYFRYKGVKAEYVNPKDAGLFVTNEPGNAQVLPESYQNLYRLRERD 174
           + + GE  NA+++A YF+  G+ A    P+D GL V+++   A+VL E+Y N+  L   D
Sbjct: 120 LASRGEHYNARIVAEYFQNSGMTARARLPEDFGLLVSDDYLGAKVLSEAYANIAELTSED 179

Query: 175 GLIIFPGFFGFSKDGDVITFSRSGSDITGSILANGLQADLYENFTDVDAVYSVNPSFVEN 234
           G+ + PGF+G ++ G+V  FSR GSD+TG  +A  + AD YEN+TDV  V+ V+PS +  
Sbjct: 180 GIAVIPGFYGVTQAGEVAVFSRGGSDLTGGEVAYAIDADTYENWTDVSGVFEVDPSLIPE 239

Query: 235 PKEISELTYREMRELSYAGFSVFHDEALIPAFRAGIPVQIKNTNNPSAEGTRVVSKRDNT 294
            + I  LT++E+R LS  GF+VFH +A++      IP+ I+NTN P   GT ++++R   
Sbjct: 240 ARAIPRLTFKEIRLLSSKGFNVFHLDAMLSCKERKIPIHIRNTNRPQEPGTIILNERVPE 299

Query: 295 NGPVVGIASDTGFCSIYISKYLMNREIGFGRRALQILEEHGLTYEHVPSGIDDMTIILRQ 354
            G +VGIA       IY+ K ++  E+GF    LQI +E  +   H P+  DD+ +++ Q
Sbjct: 300 EG-IVGIARLENMAYIYLEKDMLGEEVGFTASLLQIFQEFNINTYHYPTDKDDIAVLVNQ 358

Query: 355 GQMDAATERSVIKRIEEDLHADEVIVEHHLALIMVVGEAMRHNVGTTARAAKALSEAQVN 414
             +       + + IE+ L  D + V ++LA+I  VG  ++ N      A  ALS   + 
Sbjct: 359 DDL-TGNINDLRRHIEKKLKPDYMDVVYNLAIITPVGLGLKGNSYPIVDALLALSRNHIP 417

Query: 415 IEMINQGSSEVSMMFGVKEAEERKAVQALYQEFFAG 450
           IEMI+Q  S++    GV +A    A++ LY +   G
Sbjct: 418 IEMIDQAPSQICFHIGVSQAVADDALKILYDQLIKG 453


Lambda     K      H
   0.316    0.134    0.370 

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: 480
Number of extensions: 20
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: 454
Length of database: 455
Length adjustment: 33
Effective length of query: 421
Effective length of database: 422
Effective search space:   177662
Effective search space used:   177662
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: 51 (24.3 bits)

Align candidate WP_022948116.1 H035_RS0106110 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.9552.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-72  231.4   0.0    1.3e-72  231.2   0.0    1.0  1  lcl|NCBI__GCF_000421465.1:WP_022948116.1  H035_RS0106110 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022948116.1  H035_RS0106110 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.2   0.0   1.3e-72   1.3e-72       4     441 ..       5     451 ..       2     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: 231.2 bits;  conditional E-value: 1.3e-72
                                 TIGR00657   4 iVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAm.......agvTdaLvelaekvsseee... 62 
                                                V+KFGG+Sv+++ +i+kv +iv+++k+ +    VVvSA+       ++vTd+L+++a +  + ++   
  lcl|NCBI__GCF_000421465.1:WP_022948116.1   5 FVCKFGGSSVASAGQIEKVKQIVQADKRRR---YVVVSAPgrsrsdeQKVTDHLINIATSGAHFRDqrl 70 
                                               69*************************666...9999997444444469*********99888887566 PP

                                 TIGR00657  63 ....keliekirekhlealeela..sqalkeklkallekeleevkkereldlilsvGEklSaallaaal 125
                                                   +e  +++ ek  ++++el      + + lk++l++ le    +r  + + s+GE+  a+++a+++
  lcl|NCBI__GCF_000421465.1:WP_022948116.1  71 sitpNESKKAVLEKFTRIASELGvdAGDILASLKKDLATSLEG---DRRIAFLASRGEHYNARIVAEYF 136
                                               6666555566666666666666542333444444444444444...*********************** PP

                                 TIGR00657 126 eelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGS 194
                                               ++ g+ a++ l  + g+l ++ ++ Ak + +++ +++++l +e+ i v+ GF G+t+ ge+ +  RGGS
  lcl|NCBI__GCF_000421465.1:WP_022948116.1 137 QNSGMTARARLPEDFGLLVSDDYLGAK-VLSEAYANIAELTSEDGIAVIPGFYGVTQAGEVAVFSRGGS 204
                                               ***************************.99999999********************************* PP

                                 TIGR00657 195 DltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamra 263
                                               Dlt   +A a++Ad  e +tDV+G++  DP ++peAr ++ ++++E   L+s G  v+h +++  +++ 
  lcl|NCBI__GCF_000421465.1:WP_022948116.1 205 DLTGGEVAYAIDADTYENWTDVSGVFEVDPSLIPEARAIPRLTFKEIRLLSSKGFNVFHLDAMLSCKER 273
                                               ********************************************************************* PP

                                 TIGR00657 264 kipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakv 330
                                               kipi++++t  p+++GT+i +++++ee   + +++  +n+a + +++      +g+ a ++++ +e ++
  lcl|NCBI__GCF_000421465.1:WP_022948116.1 274 KIPIHIRNTNRPQEPGTIILNERVPEE--GIVGIARLENMAYIYLEKDMLGeeVGFTASLLQIFQEFNI 340
                                               **********************99655..899***********9999888788************9999 PP

                                 TIGR00657 331 nvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaaki 399
                                               n       ++++ i+  v+++d+    + l+++++++ +   ++v  +la+++ vG g+k++   +  +
  lcl|NCBI__GCF_000421465.1:WP_022948116.1 341 NTYHYP--TDKDDIAVLVNQDDLTGNINDLRRHIEKKLKPDYMDVVYNLAIITPVGLGLKGNSYPIVDA 407
                                               887765..88889*********99999999999************************************ PP

                                 TIGR00657 400 feaLaeeniniemissseikisvv..vdekdaekavealheklv 441
                                               + aL+++ i+iemi +   +i++   v++  a+ a++ l+++l+
  lcl|NCBI__GCF_000421465.1:WP_022948116.1 408 LLALSRNHIPIEMIDQAPSQICFHigVSQAVADDALKILYDQLI 451
                                               ***************77777776611567778889999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (455 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.19
//
[ok]

This GapMind analysis is from Apr 10 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:

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