Alignments for a candidate for asp-kinase in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Thiomicrospira cyclica ALM1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013835059.1 THICY_RS02560 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_000214825.1:WP_013835059.1
          Length = 405

 Score =  535 bits (1378), Expect = e-156
 Identities = 278/405 (68%), Positives = 332/405 (81%), Gaps = 2/405 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MALIVQK+GGTSVGT+ERI+ VA+KV KF + G  VVVV+SAMSGETNRL+ +A  +  +
Sbjct: 1   MALIVQKYGGTSVGTLERIQNVAKKVAKFVDEGHQVVVVLSAMSGETNRLVDMAKTMQSR 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
           P  RE+D++++TGEQVTIALLSMAL ++G  A+SYTG QV I TD  HTKARI  I+   
Sbjct: 61  PSKREMDMLLTTGEQVTIALLSMALQQKGYDAISYTGWQVPIQTDEVHTKARIDSINAEK 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           IR  L   +VVVVAGFQGV  NG+I+TLGRGGSDTT VALAAALKADECQIYTDVDGVYT
Sbjct: 121 IRHQLDQNKVVVVAGFQGVTANGDISTLGRGGSDTTAVALAAALKADECQIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240
           TDPRVVP+ARRL+ ITF+EMLEMASLG+KVLQIR+VEFA KY VPLRVL S Q+G GTLI
Sbjct: 181 TDPRVVPEARRLNTITFDEMLEMASLGAKVLQIRSVEFASKYQVPLRVLSSLQDGGGTLI 240

Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300
           T   EE +ME+P+ISGIAFNRDE+KL + GVPD PGVA++ILGPI+ AN+E+DMI+QN  
Sbjct: 241 T--SEENTMEKPLISGIAFNRDESKLQVLGVPDKPGVAYRILGPIADANIEIDMIIQNQG 298

Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360
            D TTDFTFTV R D   A +IL + A N+GARE + D  IAKVS+VGVGMRSH G+ASR
Sbjct: 299 QDGTTDFTFTVPRGDRAQAQDILNEVAQNLGAREVVYDDAIAKVSMVGVGMRSHVGIASR 358

Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405
           MF+ LA+E INIQMI+T+EIK+SVV++E  LE AV++LH  FELD
Sbjct: 359 MFQVLAEEDINIQMIATTEIKISVVVQEDQLEKAVKSLHLKFELD 403


Lambda     K      H
   0.317    0.133    0.362 

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: 489
Number of extensions: 13
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: 412
Length of database: 405
Length adjustment: 31
Effective length of query: 381
Effective length of database: 374
Effective search space:   142494
Effective search space used:   142494
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_013835059.1 THICY_RS02560 (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.3353533.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-143  462.8  11.7   5.9e-143  462.6  11.7    1.0  1  NCBI__GCF_000214825.1:WP_013835059.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013835059.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.6  11.7  5.9e-143  5.9e-143       1     406 [.       1     402 [.       1     403 [. 0.98

  Alignments for each domain:
  == domain 1  score: 462.6 bits;  conditional E-value: 5.9e-143
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + liVqK+GGtsvg  eri+++ak+v k + eg++vvVV+SAms++t++lv++a      +++++ +s+re+d
  NCBI__GCF_000214825.1:WP_013835059.1   1 MALIVQKYGGTSVGTLERIQNVAKKVAKFVDEGHQVVVVLSAMSGETNRLVDMA------KTMQSRPSKREMD 67 
                                           579***************************************************......9************ PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l+ +GE++++alls+al+++g++a++++g++ +i Td+ +++A+i++++  e++ ++L+++++vvvaGF+G 
  NCBI__GCF_000214825.1:WP_013835059.1  68 MLLTTGEQVTIALLSMALQQKGYDAISYTGWQVPIQTDEVHTKARIDSINA-EKIRHQLDQNKVVVVAGFQGV 139
                                           ***************************************************.********************* PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           t +G+i tLGRGGSD+tA++laaalkAd+++iyTDV+GvyttDPrvv+ea+++++i+++E+le+A+lGakvl+
  NCBI__GCF_000214825.1:WP_013835059.1 140 TANGDISTLGRGGSDTTAVALAAALKADECQIYTDVDGVYTTDPRVVPEARRLNTITFDEMLEMASLGAKVLQ 212
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvegegmlgkrgilaeifka 289
                                            r++e+a +++vp++v ss +   gTlit+   ++e++ l+++ia++++ ++l+v   g+ +k+g++ +i + 
  NCBI__GCF_000214825.1:WP_013835059.1 213 IRSVEFASKYQVPLRVLSSLQDGGGTLITSeenTMEKP-LISGIAFNRDESKLQVL--GVPDKPGVAYRILGP 282
                                           *****************************977556666.*****************..9************** PP

                             TIGR00656 290 Laeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGv 359
                                           +a+++i +d+i+q +++   t+ +++v + d  +a+++L+e+ ++++ +++ ++  +a+vs+vg+g++++ G+
  NCBI__GCF_000214825.1:WP_013835059.1 283 IADANIEIDMIIQNQGQdgtTDFTFTVPRGDRAQAQDILNEVAQNLGAREVVYDDAIAKVSMVGVGMRSHVGI 355
                                           ***************99999***************************************************** PP

                             TIGR00656 360 aseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           as++f++l+e++ini mi++ e+kisv+v+e ++ekav++lh k+e+
  NCBI__GCF_000214825.1:WP_013835059.1 356 ASRMFQVLAEEDINIQMIATTEIKISVVVQEDQLEKAVKSLHLKFEL 402
                                           ********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (405 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: 22.58
//
[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