Alignments for a candidate for asp-kinase in Caminibacter mediatlanticus TB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Caminibacter mediatlanticus TB-2

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_007474201.1 CMTB2_RS04000 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000170735.1:WP_007474201.1
          Length = 402

 Score =  441 bits (1135), Expect = e-128
 Identities = 228/403 (56%), Positives = 310/403 (76%), Gaps = 4/403 (0%)

Query: 3   LIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPV 62
           L+VQKFGGTSVG ++RIE VA  VK ++E GDD+VVV+SAM+GETN+L+D A   +  P 
Sbjct: 2   LVVQKFGGTSVGDLDRIENVANIVKSYKERGDDVVVVVSAMAGETNKLLDYANHFSKTPP 61

Query: 63  PRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKIR 122
            RE+D++VS+GE+VT ALL++AL  +G+PA++ TG Q  I T S H KARI+ ID +K++
Sbjct: 62  QREVDLLVSSGERVTSALLSIALQSKGIPAIALTGRQAGIKTTSDHTKARIMDIDPEKMQ 121

Query: 123 ADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
             LKEG+VV+VAGFQG++E+G +TTLGRGGSD T VA+A ALKAD+C+IYTDVDG+YTTD
Sbjct: 122 KHLKEGKVVIVAGFQGINENGDVTTLGRGGSDLTAVAIAGALKADKCEIYTDVDGIYTTD 181

Query: 183 PRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFK-EGPGTLIT 241
           PR+ P+A++++ I+++EMLE+ASLG+KV+Q RSVE A K NV + V  SFK E  GTLIT
Sbjct: 182 PRIEPKAKKIDVISYDEMLELASLGAKVMQSRSVELAKKLNVDIEVKSSFKPEIKGTLIT 241

Query: 242 IDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHD 301
             E + ME+ ++SGIA ++++A+++I GV D PG++ +I   ++  NI VDMIVQNV  D
Sbjct: 242 -KESKDMEKVLVSGIALDKNQARVSIFGVDDRPGISAEIFEKLANKNINVDMIVQNVGKD 300

Query: 302 NTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMF 361
              + TFTV + E E  + VL+    E     +  DT IAKVS+VGVGM+SH+GVA+  F
Sbjct: 301 GKANLTFTVPQTEVELTKEVLKE--YENNTENIEYDTDIAKVSVVGVGMKSHSGVAAKAF 358

Query: 362 EALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           + LA E+INI MISTSEIK+S+V++EKY ELAVRALH A++LD
Sbjct: 359 KTLANENINILMISTSEIKISMVIDEKYGELAVRALHKAYELD 401


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: 437
Number of extensions: 12
Number of successful extensions: 3
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: 402
Length adjustment: 31
Effective length of query: 380
Effective length of database: 371
Effective search space:   140980
Effective search space used:   140980
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_007474201.1 CMTB2_RS04000 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.2975439.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-149  484.3  14.5   1.7e-149  484.2  14.5    1.0  1  NCBI__GCF_000170735.1:WP_007474201.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170735.1:WP_007474201.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.2  14.5  1.7e-149  1.7e-149       2     406 ..       1     400 [.       1     401 [. 0.97

  Alignments for each domain:
  == domain 1  score: 484.2 bits;  conditional E-value: 1.7e-149
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 
                                           +l+VqKFGGtsvg+ +ri+++a+iv++ +++g++vvVVvSAm+++t++l++ a      + +s+ + +re d+
  NCBI__GCF_000170735.1:WP_007474201.1   1 MLVVQKFGGTSVGDLDRIENVANIVKSYKERGDDVVVVVSAMAGETNKLLDYA------NHFSKTPPQREVDL 67 
                                           79***************************************************......8************* PP

                             TIGR00656  75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147
                                           lvs GE+++salls al+ +g  a+al+g +agi T + +++A+i ++++ e++ + L+eg++v+vaGF+G +
  NCBI__GCF_000170735.1:WP_007474201.1  68 LVSSGERVTSALLSIALQSKGIPAIALTGRQAGIKTTSDHTKARIMDIDP-EKMQKHLKEGKVVIVAGFQGIN 139
                                           **************************************************.********************** PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                           e+G++TtLGRGGSDltA+++a alkAd++eiyTDV+G+yttDPr+ ++akkid isy+E+lelA+lGakv++ 
  NCBI__GCF_000170735.1:WP_007474201.1 140 ENGDVTTLGRGGSDLTAVAIAGALKADKCEIYTDVDGIYTTDPRIEPKAKKIDVISYDEMLELASLGAKVMQS 212
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskeke.egTlitn...kkensslvkaialeknvarltvegegmlgkrgilaeifka 289
                                           r++ela++ +v i+v+ss+++e +gTlit+   ++e+  lv++ial+kn+ar++++  g+ +++gi aeif+ 
  NCBI__GCF_000170735.1:WP_007474201.1 213 RSVELAKKLNVDIEVKSSFKPEiKGTLITKeskDMEK-VLVSGIALDKNQARVSIF--GVDDRPGISAEIFEK 282
                                           *****************************96533333.6*****************..9************** PP

                             TIGR00656 290 Laeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGv 359
                                           La+++invd+i+q  ++    +++++v +++v+ +k++Lke+ +++  e++e++ d+a+vs+vg+g+++++Gv
  NCBI__GCF_000170735.1:WP_007474201.1 283 LANKNINVDMIVQNVGKdgkANLTFTVPQTEVELTKEVLKEYENNT--ENIEYDTDIAKVSVVGVGMKSHSGV 353
                                           *************98877779*********************7555..5************************ PP

                             TIGR00656 360 aseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           a+++fk l+++ninilmis+se+kis+++dek+ e avr+lh+++e+
  NCBI__GCF_000170735.1:WP_007474201.1 354 AAKAFKTLANENINILMISTSEIKISMVIDEKYGELAVRALHKAYEL 400
                                           ********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (402 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: 29.64
//
[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