Alignments for a candidate for asp-kinase in Methanospirillum lacunae Ki8-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methanospirillum lacunae Ki8-1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_109969877.1 DK846_RS15330 aspartate kinase

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_003173355.1:WP_109969877.1
          Length = 467

 Score =  397 bits (1021), Expect = e-115
 Identities = 215/470 (45%), Positives = 297/470 (63%), Gaps = 15/470 (3%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60
           M  +MKFGGTSV + + +     I+T    + D +VVVVSA   VT+ ++E ++Q +  R
Sbjct: 1   MKLIMKFGGTSVQNADAVGKTMDIITSHLAKGDQMVVVVSAQRGVTDRIIETAEQMVSSR 60

Query: 61  DIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPK 120
           D + V   + ++   H   ++    + +   E  ++I   I  L   L  V +L ELTP+
Sbjct: 61  DTSAVNVLVDYLTSTHLTTLQAV--APDYYSETSEVIIRAINNLHDFLHAVFHLRELTPR 118

Query: 121 SRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSA---RVKRLEVKER 177
           SRDY++SFGERL++PI+S A+R  G  S+AL+G EAGI+T  N G A         ++ R
Sbjct: 119 SRDYVISFGERLNAPIISAALRQRGISSLALDGCEAGILTTGNHGDAIALPAGEARIRSR 178

Query: 178 LLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYT 237
           L PL+   + PVV GF+G TE+G +TTLGR GSDY+AA++G  L  D I IWTDV G+ T
Sbjct: 179 LDPLITTSV-PVVMGFMGCTEKGVVTTLGRSGSDYTAAILGAALMVDEIWIWTDVDGIMT 237

Query: 238 TDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTL 297
           TDPRLV  AR IP++SYIE MEL+YFGAKV+H R+IEPAM+K IP+ VKNTF P   GT 
Sbjct: 238 TDPRLVKDARVIPRISYIEVMELSYFGAKVMHSRSIEPAMQKNIPVWVKNTFNPSYPGTC 297

Query: 298 ITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSS 357
           I         +VKAI+ I  VA I I GA M+G  G A  IF  L E ++NV++ISQGSS
Sbjct: 298 IEKGERRETRVVKAITFIDKVAAITITGAQMIGRPGVAKHIFSILAENQINVMMISQGSS 357

Query: 358 ETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGA 417
           E NISL++ E+ V  A  AL         +      + R+++ ++DVC ++VVG+GM G 
Sbjct: 358 EANISLIIEEKQVQTAKDAL---------QPLKERCVFREITANEDVCAVAVVGSGMAGM 408

Query: 418 KGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKF 467
            G AG+ F+A+ ++G N  MI+QGSSEVNISFV+ ++D    V  LHE+F
Sbjct: 409 AGTAGRTFSALGKAGINAMMISQGSSEVNISFVVKQEDGPRAVMVLHEEF 458


Lambda     K      H
   0.316    0.135    0.364 

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: 547
Number of extensions: 20
Number of successful extensions: 6
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: 473
Length of database: 467
Length adjustment: 33
Effective length of query: 440
Effective length of database: 434
Effective search space:   190960
Effective search space used:   190960
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_109969877.1 DK846_RS15330 (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.3250657.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-135  439.0   5.3   1.3e-135  438.9   5.3    1.0  1  NCBI__GCF_003173355.1:WP_109969877.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003173355.1:WP_109969877.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.9   5.3  1.3e-135  1.3e-135       3     441 ..       2     459 ..       1     460 [. 0.95

  Alignments for each domain:
  == domain 1  score: 438.9 bits;  conditional E-value: 1.3e-135
                             TIGR00657   3 liVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekire 71 
                                           ++++KFGGtSv n++ + k  +i++++ +kg+q+vVVvSA  gvTd+ +e+ae++ s ++    + l++ + +
  NCBI__GCF_003173355.1:WP_109969877.1   2 KLIMKFGGTSVQNADAVGKTMDIITSHLAKGDQMVVVVSAQRGVTDRIIETAEQMVSSRDtsavNVLVDYLTS 74 
                                           679****************************************************999997776566777889 PP

                             TIGR00657  72 khlealeelasqalkeklkallekeleevkk...........ereldlilsvGEklSaallaaaleelgvkav 133
                                           +hl++l+++a++  +e+++ ++ +  ++              +r++d+++s+GE+l a++++aal+++g+ ++
  NCBI__GCF_003173355.1:WP_109969877.1  75 THLTTLQAVAPDYYSETSEVIIRAINNLHDFlhavfhlreltPRSRDYVISFGERLNAPIISAALRQRGISSL 147
                                           9999999999877777777777666666555778999************************************ PP

                             TIGR00657 134 sllgaeagiltdsefgrAk...vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAa 203
                                           +l g eagilt++++g+A    + e  +++rl++l++   ++vv GF+G tekg +ttLGR GSD+tAa+l+a
  NCBI__GCF_003173355.1:WP_109969877.1 148 ALDGCEAGILTTGNHGDAIalpAGEARIRSRLDPLITTS-VPVVMGFMGCTEKGVVTTLGRSGSDYTAAILGA 219
                                           *******************88777888889999988887.********************************* PP

                             TIGR00657 204 alkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276
                                           al  de++i+tDVdGi+t+DPr+v++Ar ++ isy E +EL+++Gakv+h r++epam+++ip+ vk+tfnp+
  NCBI__GCF_003173355.1:WP_109969877.1 220 ALMVDEIWIWTDVDGIMTTDPRLVKDARVIPRISYIEVMELSYFGAKVMHSRSIEPAMQKNIPVWVKNTFNPS 292
                                           ************************************************************************* PP

                             TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfv 347
                                            +GT i + +  +e+  vka+++ ++ a +++ g++m   pg+++++f++lae+++nv++i+q sse +is++
  NCBI__GCF_003173355.1:WP_109969877.1 293 YPGTCIEKGER-RETRVVKAITFIDKVAAITITGAQMIgrPGVAKHIFSILAENQINVMMISQGSSEANISLI 364
                                           *******9977.777**********************999********************************* PP

                             TIGR00657 348 vdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..ssei 418
                                           ++++++++ak +l + +ke   ++e++ +++++ v++vG+gm++  g a++ f+aL +++in +mis  sse+
  NCBI__GCF_003173355.1:WP_109969877.1 365 IEEKQVQTAKDAL-QPLKERCVFREITANEDVCAVAVVGSGMAGMAGTAGRTFSALGKAGINAMMISqgSSEV 436
                                           ************8.68********************************************************* PP

                             TIGR00657 419 kisvvvdekdaekavealheklv 441
                                           +is+vv+++d+ +av +lhe+++
  NCBI__GCF_003173355.1:WP_109969877.1 437 NISFVVKQEDGPRAVMVLHEEFE 459
                                           ********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (467 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: 29.70
//
[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