Alignments for a candidate for asp-kinase in Halococcus hamelinensis 100A6

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Halococcus hamelinensis 100A6

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_007690747.1 C447_RS02970 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000336675.1:WP_007690747.1
          Length = 393

 Score =  164 bits (416), Expect = 3e-45
 Identities = 129/412 (31%), Positives = 206/412 (50%), Gaps = 36/412 (8%)

Query: 4   IVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPVP 63
           +V KFGGTS+GS  R+ + A+ V    EAG ++ VV+SAM   T+ L+   ++I  +   
Sbjct: 3   VVAKFGGTSLGSGSRVNRAADSVAAAVEAGHEIAVVVSAMGSTTDYLL---REIQFEADE 59

Query: 64  RELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVR--ILTDSSHNKARILQIDDQKI 121
            +   IVS GE+ +  ++  AL  RGV A           ++TDS             + 
Sbjct: 60  ADRAEIVSMGERTSARMVKAALSARGVDATFLEPGSEHWPVVTDSRGEVDVEETTRRAQA 119

Query: 122 RADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTT 181
            AD  +G V +V GF   D  G++TTLGRGGSDTT V L   + ADE  I TDV+GV T 
Sbjct: 120 LADQLDGMVPIVTGFLAEDHAGAVTTLGRGGSDTTAVMLGNYMSADEVVIVTDVEGVMTG 179

Query: 182 DPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEG------ 235
           DPRVV  AR + KI+ +E+  ++  G++V+   ++ +    ++ +RV+H ++ G      
Sbjct: 180 DPRVVEGARNVAKISVDELRNLSFRGAEVIAPSALNYK-TTDLSVRVVH-YQHGDLLQGG 237

Query: 236 ---PGTLITIDEEESMEQPIISGIAFNRDEAKLTI--RGVPDTPGVAFKILGPISASNIE 290
               GT  T+ + +  E+P+          A LT+  R + + PG+   + G +S ++I 
Sbjct: 238 THIEGTFETLIDLQ--EEPL----------ACLTVAGRAIRNRPGILAALSGALSEADIN 285

Query: 291 VDMIVQNVAHDNTTDFTFTVHRNEYEKAQSVL-ENTAREIGAREVIGDTKIAKVSIVGVG 349
           +D      A       TF V+  E  +A++VL E    E     V  D ++A + + G  
Sbjct: 286 ID-----AAASGLDSVTFYVYSRESTEAETVLHERVINEDALSSVTVDEEVAALRVTGGE 340

Query: 350 MRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAF 401
           + + +GV   M E LA E I +  + TS   V+V ++    E A+  +   F
Sbjct: 341 LPTQSGVVQGMIETLADERIAVHDVITSATSVAVFVDWDDREQALSVIQDTF 392


Lambda     K      H
   0.316    0.133    0.358 

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: 341
Number of extensions: 18
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: 411
Length of database: 393
Length adjustment: 31
Effective length of query: 380
Effective length of database: 362
Effective search space:   137560
Effective search space used:   137560
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_007690747.1 C447_RS02970 (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.2228961.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-85  274.1  10.4    5.3e-72  229.2   2.9    2.0  2  NCBI__GCF_000336675.1:WP_007690747.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000336675.1:WP_007690747.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.7   8.9e-18   8.9e-18       2      52 ..       1      51 [.       1      56 [. 0.95
   2 !  229.2   2.9   5.3e-72   5.3e-72     100     440 ..      56     392 ..      50     393 .] 0.88

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 8.9e-18
                             TIGR00657  2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLve 52
                                          +++V+KFGGtS+g++ r++++a+ v ++ e g++ +VVvSAm+++Td L+ 
  NCBI__GCF_000336675.1:WP_007690747.1  1 MRVVAKFGGTSLGSGSRVNRAADSVAAAVEAGHEIAVVVSAMGSTTDYLLR 51
                                          689********************************************9986 PP

  == domain 2  score: 229.2 bits;  conditional E-value: 5.3e-72
                             TIGR00657 100 vkkereldlilsvGEklSaallaaaleelgvka..vsllgaeagiltdsefgrAkvleeikterleklleeg. 169
                                           +  e+++++i+s+GE++Sa++++aal+++gv+a  ++    +++++tds+ +  +   e++t+r ++l ++  
  NCBI__GCF_000336675.1:WP_007690747.1  56 EADEADRAEIVSMGERTSARMVKAALSARGVDAtfLEPGSEHWPVVTDSRGEVDV---EETTRRAQALADQLd 125
                                           345899************************96611456678999****9755544...444444444443322 PP

                             TIGR00657 170 .iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEa 241
                                            ++++v+GF++ ++ g +ttLGRGGSD+tA++l++ + Adev i+tDV+G++t DPr+v+ Ar +++is++E 
  NCBI__GCF_000336675.1:WP_007690747.1 126 gMVPIVTGFLAEDHAGAVTTLGRGGSDTTAVMLGNYMSADEVVIVTDVEGVMTGDPRVVEGARNVAKISVDEL 198
                                           49*********************************************************************** PP

                             TIGR00657 242 lELaslGakvLhprtlepamr.akipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttm 313
                                            +L+  Ga+v+ p +l++    +++++v  ++++  ++GT i ++ +      +  l+ ++  a ++v+g   
  NCBI__GCF_000336675.1:WP_007690747.1 199 RNLSFRGAEVIAPSALNYKTTdLSVRVVHYQHGDLLQGGTHIEGTFE--T---LIDLQ-EEPLACLTVAGRAI 265
                                           ******************9988**********************955..2...22233.34456667777666 PP

                             TIGR00657 314 k..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvsl 384
                                           +  pgila + gal+ea++n+d+ +  s+ +s++f v  ++  +a+++l++ v +e+al++v+v++++a   +
  NCBI__GCF_000336675.1:WP_007690747.1 266 RnrPGILAALSGALSEADINIDAAA--SGLDSVTFYVYSRESTEAETVLHERVINEDALSSVTVDEEVAALRV 336
                                           668********************99..55559***************************************** PP

                             TIGR00657 385 vGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhekl 440
                                            G ++ ++ gv++ ++e+La+e i ++ + +s +++ v+vd++d e+a+ ++++ +
  NCBI__GCF_000336675.1:WP_007690747.1 337 TGGELPTQSGVVQGMIETLADERIAVHDVITSATSVAVFVDWDDREQALSVIQDTF 392
                                           **************************************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (393 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.32
//
[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