Alignments for a candidate for asp-kinase in Cereibacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Cereibacter sphaeroides ATCC 17029

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011337028.1 RSPH17029_RS02525 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000015985.1:WP_011337028.1
          Length = 419

 Score =  406 bits (1043), Expect = e-118
 Identities = 221/417 (52%), Positives = 296/417 (70%), Gaps = 14/417 (3%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           M L+V KFGGTSV  + RI+  A+KVK+  E G D++V++SAMSG+TN L+   +Q +  
Sbjct: 1   MPLLVMKFGGTSVADLARIKNAAQKVKREVERGYDVIVIVSAMSGKTNELVGWVEQTSPL 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
              RE D +VS+GE VT  L+ + L +  VPA S+ G QV I T S H+ AR L+I  + 
Sbjct: 61  FDAREYDAVVSSGENVTAGLMALTLQEMEVPARSWQGWQVPIRTTSQHSAARFLEIPREN 120

Query: 121 IRADLKEG-RVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           + A   EG +V VVAGFQGV   G ITTLGRGGSDTT VA AAA  A+ C IYTDVDGVY
Sbjct: 121 LDAKFAEGFKVAVVAGFQGVSPEGRITTLGRGGSDTTAVAFAAAFAAERCDIYTDVDGVY 180

Query: 180 TTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFK---EGP 236
           TTDPR+  +AR+LEKI +EEMLE+ASLG+KVLQ RSVE A +Y V LRVL SF+   E  
Sbjct: 181 TTDPRIASKARKLEKIAYEEMLELASLGAKVLQTRSVELAMRYKVKLRVLSSFEDTDETS 240

Query: 237 GTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQ 296
           GTL+  DEE+ ME  ++SG+A++RDEAK+T+  V D PGVA  I GP++ + + VDMIVQ
Sbjct: 241 GTLV-CDEEDIMESKVVSGVAYSRDEAKMTLVTVEDRPGVAAAIFGPLAEAGVNVDMIVQ 299

Query: 297 NVAH-------DNTTDFTFTVHRNEYEKAQSVLENTARE--IGAREVIGDTKIAKVSIVG 347
           N++         + TD TF+   N+  +A+  LE+   E  I   +++ DT++AKVS+VG
Sbjct: 300 NISEKDYGSHPGSVTDMTFSCPINQVARARKALEDAKAEGTIVYDDLVVDTEVAKVSVVG 359

Query: 348 VGMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           +GMRSHAGVA+ MF+ALA + +NI++I+TSEIK+SV+++ KY+ELAV+ALH AF L+
Sbjct: 360 IGMRSHAGVAATMFKALAADGVNIKVIATSEIKISVLIDRKYMELAVQALHDAFALE 416


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: 422
Number of extensions: 21
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: 411
Length of database: 419
Length adjustment: 31
Effective length of query: 380
Effective length of database: 388
Effective search space:   147440
Effective search space used:   147440
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_011337028.1 RSPH17029_RS02525 (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.3139157.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.4e-128  413.6   8.2     5e-128  413.5   8.2    1.0  1  NCBI__GCF_000015985.1:WP_011337028.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015985.1:WP_011337028.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.5   8.2    5e-128    5e-128       3     406 ..       3     415 ..       1     416 [. 0.96

  Alignments for each domain:
  == domain 1  score: 413.5 bits;  conditional E-value: 5e-128
                             TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                           l V+KFGGtsv++  rik+aa++v++e+++g++v+V+vSAms++t+elv  +      e++s     re d +
  NCBI__GCF_000015985.1:WP_011337028.1   3 LLVMKFGGTSVADLARIKNAAQKVKREVERGYDVIVIVSAMSGKTNELVGWV------EQTSPLFDAREYDAV 69 
                                           89**************************************************......7999999******** PP

                             TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeeg.iivvvaGFiGat 147
                                           vs GE +++ l++  l+e +v a++ +g++ +i+T +++  A+  e+   e+L    +eg ++ vvaGF+G  
  NCBI__GCF_000015985.1:WP_011337028.1  70 VSSGENVTAGLMALTLQEMEVPARSWQGWQVPIRTTSQHSAARFLEIPR-ENLDAKFAEGfKVAVVAGFQGVS 141
                                           ***********************************************99.99999999985699********* PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                            eG+iTtLGRGGSD+tA++ aaa  A+r++iyTDV+GvyttDPr+ ++a+k++ki+yeE+lelA+lGakvl+ 
  NCBI__GCF_000015985.1:WP_011337028.1 142 PEGRITTLGRGGSDTTAVAFAAAFAAERCDIYTDVDGVYTTDPRIASKARKLEKIAYEEMLELASLGAKVLQT 214
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskeke...egTlitn..kkensslvkaialeknvarltvegegmlgkrgilaeifk 288
                                           r++ela+++kv+++v ss+e     +gTl+++  +  +s++v+++a++++ a++t++   + +++g++a if+
  NCBI__GCF_000015985.1:WP_011337028.1 215 RSVELAMRYKVKLRVLSSFEDTdetSGTLVCDeeDIMESKVVSGVAYSRDEAKMTLV--TVEDRPGVAAAIFG 285
                                           ****************9987543368*****966333446*****************..9************* PP

                             TIGR00656 289 aLaeeeinvdlisqtese..........tsislvvdeedvdeakkaLkeesgaae...lesleveedlavvsi 348
                                            Lae+++nvd+i+q  se          t+++++   ++v +a kaL++ + + +   +++l v+ ++a+vs+
  NCBI__GCF_000015985.1:WP_011337028.1 286 PLAEAGVNVDMIVQNISEkdygshpgsvTDMTFSCPINQVARARKALEDAKAE-GtivYDDLVVDTEVAKVSV 357
                                           *****************99*******99*********************9744.3599*************** PP

                             TIGR00656 349 vgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           vg g++++ Gva+ +fkal+ +++ni+ i++se+kisvl+d k++e av++lh+++ +
  NCBI__GCF_000015985.1:WP_011337028.1 358 VGIGMRSHAGVAATMFKALAADGVNIKVIATSEIKISVLIDRKYMELAVQALHDAFAL 415
                                           ******************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (419 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: 00:00:00.00
# Mc/sec: 20.27
//
[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