Alignments for a candidate for asp-kinase in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Chlorobium phaeobacteroides BS1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012475797.1 CPHAMN1_RS12085 lysine-sensitive aspartokinase 3

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000020545.1:WP_012475797.1
          Length = 471

 Score =  327 bits (839), Expect = 4e-94
 Identities = 197/479 (41%), Positives = 298/479 (62%), Gaps = 30/479 (6%)

Query: 4   VMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIA 63
           VMKFGGTS+G+   ++   +IV  R+KE +  +VV+SA S +TN L++I++ A D R + 
Sbjct: 3   VMKFGGTSIGTASAMKRAMQIVG-REKEKNIPLVVLSACSGITNRLIQIAEAAGDSR-LD 60

Query: 64  KVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRD 123
           +       +RE H + +EE I    +++ +K+ +D+ I EL+ ++ GV  +GELT +S D
Sbjct: 61  EAMRLSGEVREHHLELVEELINDASLRQSLKEKVDAYIGELDMLIQGVDIVGELTARSFD 120

Query: 124 YILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSAR----VKRLEVKERLL 179
              SFGE LS+ + S A+R+ G  ++  +  E  +ITD+NF +AR    +    V+  L 
Sbjct: 121 TFCSFGELLSTTVFSDAMREAGYDTVWKDIREV-MITDDNFSAARPFEDLCEKNVQNSLR 179

Query: 180 PLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTD 239
           PLL++G I V  GFIG+T +G  TT+GRGGSDY+AAL+G  L +D I+IWTDV GV T D
Sbjct: 180 PLLEQGSIVVTQGFIGSTRDGKTTTMGRGGSDYTAALLGAWLPSDEIQIWTDVDGVMTCD 239

Query: 240 PRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLIT 299
           PR+VP AR I  +++ EA EL+Y GAKVLHP TI PA+++ IP+ V N+  PES+GT+IT
Sbjct: 240 PRIVPDARSIRVMTFTEAAELSYLGAKVLHPDTIAPAVKQNIPVYVLNSLCPESKGTVIT 299

Query: 300 NDMEMSD-----SIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQ 354
           N+ E  +      +VK+I+  K   +IN     M+G  G  A IF       V+V ++S 
Sbjct: 300 NNPETLEGMSYGGLVKSIAVKKGQCIINFRSNRMLGRHGFMADIFGVFARAGVSVEMVS- 358

Query: 355 GSSETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGM 414
            +SE ++SL VSE        +L++   D  K        + +V ++ DV  ISVVG  +
Sbjct: 359 -TSEVSVSLTVSES------ASLEQLLDDLRK--------MGEVEIEPDVATISVVGDNL 403

Query: 415 RGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKTNS 473
           R AKG+AG+IF+A+ +   NI+MI+QG+SE+N+ FV++ +D+   V+ LH +F     S
Sbjct: 404 RTAKGMAGRIFSAMKD--VNIRMISQGASEINVGFVVEGEDVFRAVQHLHHEFFSDIES 460


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: 521
Number of extensions: 22
Number of successful extensions: 8
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: 471
Length adjustment: 33
Effective length of query: 440
Effective length of database: 438
Effective search space:   192720
Effective search space used:   192720
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_012475797.1 CPHAMN1_RS12085 (lysine-sensitive aspartokinase 3)
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.13409.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-124  401.0   0.8   4.5e-124  400.8   0.8    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012475797.1  CPHAMN1_RS12085 lysine-sensitive


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012475797.1  CPHAMN1_RS12085 lysine-sensitive aspartokinase 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.8   0.8  4.5e-124  4.5e-124       5     441 ..       3     455 ..       1     456 [. 0.95

  Alignments for each domain:
  == domain 1  score: 400.8 bits;  conditional E-value: 4.5e-124
                                 TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekir 70 
                                               V+KFGGtS+g++  +k++ +iv +ekek+  ++VV+SA +g+T++L+++ae + + +    ++l  ++r
  lcl|NCBI__GCF_000020545.1:WP_012475797.1   3 VMKFGGTSIGTASAMKRAMQIVGREKEKN-IPLVVLSACSGITNRLIQIAEAAGDSRLdeaMRLSGEVR 70 
                                               9*************************777.99*********************99998776666779** PP

                                 TIGR00657  71 ekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaale 126
                                               e+hle +eel+   +l++ lk+ +++ + e+               r++d+  s+GE lS+++++ a++
  lcl|NCBI__GCF_000020545.1:WP_012475797.1  71 EHHLELVEELInDASLRQSLKEKVDAYIGELDMliqgvdivgeltARSFDTFCSFGELLSTTVFSDAMR 139
                                               ***********77788899999999998888888999******************************** PP

                                 TIGR00657 127 elgvkavsllgaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGR 191
                                               e g  +  + +++++++td++f+ A+      e+  ++ l +lle+g ivv++GFiG+t++g++tt+GR
  lcl|NCBI__GCF_000020545.1:WP_012475797.1 140 EAG-YDTVWKDIREVMITDDNFSAARpfedLCEKNVQNSLRPLLEQGSIVVTQGFIGSTRDGKTTTMGR 207
                                               ***.777789****************999888899999******************************* PP

                                 TIGR00657 192 GGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepa 260
                                               GGSD+tAall+a l  de++i+tDVdG++t+DPrivp+Ar +  +++ Ea+EL++lGakvLhp+t+ pa
  lcl|NCBI__GCF_000020545.1:WP_012475797.1 208 GGSDYTAALLGAWLPSDEIQIWTDVDGVMTCDPRIVPDARSIRVMTFTEAAELSYLGAKVLHPDTIAPA 276
                                               ********************************************************************* PP

                                 TIGR00657 261 mrakipivvkstfnpeaeGTlivaksk....seeepavkalsldknqalvsvsgttmk..pgilaevfg 323
                                               ++++ip+ v ++  pe++GT+i+++ +    ++    vk+++++k q +++ +++ m    g++a++fg
  lcl|NCBI__GCF_000020545.1:WP_012475797.1 277 VKQNIPVYVLNSLCPESKGTVITNNPEtlegMSYGGLVKSIAVKKGQCIINFRSNRMLgrHGFMADIFG 345
                                               *************************9999999999**********************999********* PP

                                 TIGR00657 324 alaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksa 392
                                                 a+a+v+v++++  +se s+s++v+++   + ++l    ++++++++eve+e ++a++s+vG+++++a
  lcl|NCBI__GCF_000020545.1:WP_012475797.1 346 VFARAGVSVEMVS--TSEVSVSLTVSESA--SLEQL----LDDLRKMGEVEIEPDVATISVVGDNLRTA 406
                                               ************9..8888999*998764..44555....568999*********************** PP

                                 TIGR00657 393 pgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               +g+a++if+a+++  +ni+mis  +sei++ +vv+++d+ +av+ lh++++
  lcl|NCBI__GCF_000020545.1:WP_012475797.1 407 KGMAGRIFSAMKD--VNIRMISqgASEINVGFVVEGEDVFRAVQHLHHEFF 455
                                               ***********99..**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (471 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: 12.57
//
[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