Alignments for a candidate for asp-kinase in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Leptospirillum ferrooxidans C2-3

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_014449307.1 LFE_RS05800 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000284315.1:WP_014449307.1
          Length = 417

 Score =  453 bits (1165), Expect = e-132
 Identities = 238/407 (58%), Positives = 309/407 (75%), Gaps = 3/407 (0%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQKFGGTSVGS+ERI  VA  V+K   +GD +VVV+SAM+GET+RL+ LA  +S D
Sbjct: 1   MALIVQKFGGTSVGSIERIRLVAGIVQKTLSSGDQVVVVVSAMAGETDRLVKLAHELSPD 60

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
             P  RE+D+++S+GE+VT ALLA+ LN  G+PA S TG QV I TD+ HTKARI  I  
Sbjct: 61  --PPEREMDMLMSSGERVTSALLAICLNNMGIPARSMTGRQVGIKTDNVHTKARIESISS 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           + +   L+AG V +VAGFQG+  Q N+TTLGRGGSDTT VA+A A+ A  C IYTDV GV
Sbjct: 119 EPLAQSLEAGIVPIVAGFQGISPQENVTTLGRGGSDTTAVAIAVAIGAQRCDIYTDVTGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240
           +TTDP +V  A+++D+I +EEMLEMASLG+KVLQ R+VEFA KY +P+RV  +F + PGT
Sbjct: 179 FTTDPNLVPQARKIDRIAYEEMLEMASLGAKVLQTRSVEFAMKYKMPVRVRSTFSDDPGT 238

Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300
           L+T +EE+ MEQ ++SG+  ++++AK+T+  VPD PG+A ++   ISG +I VDMIVQN+
Sbjct: 239 LVT-EEEKGMEQIVVSGVTLDKNQAKITVSDVPDRPGLAARLFEDISGHSIIVDMIVQNI 297

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
             D  TD +FTV R+E   AERI  + +KEIGA E+     I K+SIVGVGMRSH+GVA+
Sbjct: 298 GQDQMTDISFTVPRSESRKAERIALDFSKEIGAGEIRVKEDIVKISIVGVGMRSHSGVAA 357

Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 407
           RMF ALAKE INI MISTSEIK+S +IE++Y EL+VR LH  FEL++
Sbjct: 358 RMFSALAKEGINIVMISTSEIKISCLIEDRYAELSVRTLHKEFELES 404


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: 465
Number of extensions: 16
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: 417
Length adjustment: 31
Effective length of query: 382
Effective length of database: 386
Effective search space:   147452
Effective search space used:   147452
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_014449307.1 LFE_RS05800 (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.3552.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-146  474.4  12.1     2e-143  464.6  12.1    2.0  1  lcl|NCBI__GCF_000284315.1:WP_014449307.1  LFE_RS05800 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000284315.1:WP_014449307.1  LFE_RS05800 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.6  12.1    2e-143    2e-143       1     441 [.       1     401 [.       1     402 [. 0.98

  Alignments for each domain:
  == domain 1  score: 464.6 bits;  conditional E-value: 2e-143
                                 TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 
                                               maliVqKFGGtSvg++eri+ va iv+k+  +g+qvvVVvSAmag Td+Lv+la+++s+++        
  lcl|NCBI__GCF_000284315.1:WP_014449307.1   1 MALIVQKFGGTSVGSIERIRLVAGIVQKTLSSGDQVVVVVSAMAGETDRLVKLAHELSPDP-------- 61 
                                               89***********************************************************........ PP

                                 TIGR00657  70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138
                                                           +                    ere+d+++s+GE++++alla  l++ g+ a+s++g 
  lcl|NCBI__GCF_000284315.1:WP_014449307.1  62 ------------P--------------------EREMDMLMSSGERVTSALLAICLNNMGIPARSMTGR 98 
                                               ............7....................8*********************************** PP

                                 TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                               + gi td+ +++A+ +e+i++e l++ le+gi+++vaGF+G++++ ++ttLGRGGSD+tA+++A a++A
  lcl|NCBI__GCF_000284315.1:WP_014449307.1  99 QVGIKTDNVHTKAR-IESISSEPLAQSLEAGIVPIVAGFQGISPQENVTTLGRGGSDTTAVAIAVAIGA 166
                                               **************.****************************************************** PP

                                 TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276
                                               ++++iytDV G++t+DP++vp+Ar++d i+yeE+lE+aslGakvL+ r++e+am++k p++v+stf+++
  lcl|NCBI__GCF_000284315.1:WP_014449307.1 167 QRCDIYTDVTGVFTTDPNLVPQARKIDRIAYEEMLEMASLGAKVLQTRSVEFAMKYKMPVRVRSTFSDD 235
                                               ********************************************************************* PP

                                 TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343
                                                +GTl+++++k +e+  v++++ldknqa+++vs ++++pg +a++f+ ++ +++ vd+i+q++++++  
  lcl|NCBI__GCF_000284315.1:WP_014449307.1 236 -PGTLVTEEEKGMEQIVVSGVTLDKNQAKITVSDVPDRPGLAARLFEDISGHSIIVDMIVQNIGQDQmt 303
                                               .**********9999*************************************************66667 PP

                                 TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411
                                                isf+v++++  ka+++    + +e   +e++v++++ ++s+vG gm+s+ gvaa++f+aLa+e+ini+
  lcl|NCBI__GCF_000284315.1:WP_014449307.1 304 dISFTVPRSESRKAERIAL-DFSKEIGAGEIRVKEDIVKISIVGVGMRSHSGVAARMFSALAKEGINIV 371
                                               9****************75.6************************************************ PP

                                 TIGR00657 412 missseikisvvvdekdaekavealheklv 441
                                               mis+seikis+++++++ae  v++lh++++
  lcl|NCBI__GCF_000284315.1:WP_014449307.1 372 MISTSEIKISCLIEDRYAELSVRTLHKEFE 401
                                               ***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 3.41
//
[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