GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Lentibacillus jeotgali Grbi

Align diaminopimelate decarboxylase subunit (EC 4.1.1.20) (characterized)
to candidate WP_010530863.1 ON01_RS09805 diaminopimelate decarboxylase

Query= metacyc::MONOMER-6601
         (439 letters)



>NCBI__GCF_000224785.1:WP_010530863.1
          Length = 435

 Score =  558 bits (1439), Expect = e-164
 Identities = 264/425 (62%), Positives = 338/425 (79%)

Query: 10  NQHGHLEIGGVDALYLAEKYGTPLYVYDVALIRERAKSFKQAFISAGLKAQVAYASKAFS 69
           N+ GHL IGG+D++ LAEKYGTPLYVYDV+LIRE  ++F + F   G+ AQVAYASKAFS
Sbjct: 11  NEAGHLAIGGIDSVALAEKYGTPLYVYDVSLIRENCRAFVETFRELGVPAQVAYASKAFS 70

Query: 70  SVAMIQLAEEEGLSLDVVSGGELYTAVAAGFPAERIHFHGNNKSREELRMALEHRIGCIV 129
           SVAM+Q+ ++EGLSLDVVS GELYTA+ AGFPA++IH HGNNKS +EL MA+E+ IGCIV
Sbjct: 71  SVAMLQVIKQEGLSLDVVSQGELYTALEAGFPADKIHMHGNNKSIDELEMAIEYDIGCIV 130

Query: 130 VDNFYEIALLEDLCKETGHSIDVLLRITPGVEAHTHDYITTGQEDSKFGFDLHNGQTERA 189
            DNFYEI L+  + +    +++VL+R+TPG+E +THDYI TG EDSKFGF+L NGQ + A
Sbjct: 131 ADNFYEIELINSILQRKNKAMNVLMRVTPGIEPNTHDYIVTGNEDSKFGFNLANGQADEA 190

Query: 190 IEQVLQSEHIQLLGVHCHIGSQIFDTAGFVLAAEKIFKKLDEWRDSYSFVSKVLNLGGGF 249
             Q+ +SEHIQ  G+H HIGSQ+F+T   +LAA+ +F+KL EW + Y +  +VLNLGGGF
Sbjct: 191 FLQLQRSEHIQFKGLHSHIGSQLFETEEILLAAKVLFQKLAEWHEKYDYTPEVLNLGGGF 250

Query: 250 GIRYTEDDEPLHATEYVEKIIEAVKENASRYGFDIPEIWIEPGRSLVGDAGTTLYTVGSQ 309
           GIRYT++D+PL  + +V+++   V+E A+ +   +PEIWIEPGR++ G+AG TLYTVGS 
Sbjct: 251 GIRYTQEDKPLDYSVHVKELSVVVQEQAAYFNLPLPEIWIEPGRAIAGNAGITLYTVGSI 310

Query: 310 KEVPGVRQYVAVDGGMNDNIRPALYQAKYEAAAANRIGEAHDKTVSIAGKCCESGDMLIW 369
           KE+PGVR YVAVDGGM DNIRPALY AKYE   AN+  +    TVSIAGKCCESGDML+W
Sbjct: 311 KEIPGVRHYVAVDGGMTDNIRPALYNAKYEGVLANKAAQPVTDTVSIAGKCCESGDMLMW 370

Query: 370 DIDLPEVKEGDLLAVFCTGAYGYSMANNYNRIPRPAVVFVENGEAHLVVKRETYEDIVKL 429
           D+ +P V+  D+LAVF TGAYGYSMAN+YNR  + AVVFVENG  HLVV+RE+Y+D+VK 
Sbjct: 371 DLPVPAVESNDILAVFSTGAYGYSMANHYNRFAKAAVVFVENGRDHLVVQRESYQDVVKN 430

Query: 430 DLPFK 434
           DL ++
Sbjct: 431 DLSYE 435


Lambda     K      H
   0.319    0.137    0.401 

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: 593
Number of extensions: 22
Number of successful extensions: 1
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: 439
Length of database: 435
Length adjustment: 32
Effective length of query: 407
Effective length of database: 403
Effective search space:   164021
Effective search space used:   164021
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_010530863.1 ON01_RS09805 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.1909909.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-147  476.6   0.1     3e-147  476.4   0.1    1.0  1  NCBI__GCF_000224785.1:WP_010530863.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010530863.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.4   0.1    3e-147    3e-147       4     416 ..      11     431 ..       8     432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 476.4 bits;  conditional E-value: 3e-147
                             TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka..eeslvlYAvKAnsnlavlrllaeeGl 74 
                                           ++ g+l i+g+d  +lae++gtPlYvyd + +re+++a+ e f++    ++v+YA+KA+s++a+l+++++eGl
  NCBI__GCF_000224785.1:WP_010530863.1  11 NEAGHLAIGGIDSVALAEKYGTPLYVYDVSLIRENCRAFVETFRElgVPAQVAYASKAFSSVAMLQVIKQEGL 83 
                                           789****************************************9975556*********************** PP

                             TIGR01048  75 gldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllR 147
                                           +ldvvs+GEl++al+Ag++a+ki+ +gn+ks +ele+a+e++i +i++d++ e+el+++i ++ +k ++vl+R
  NCBI__GCF_000224785.1:WP_010530863.1  84 SLDVVSQGELYTALEAGFPADKIHMHGNNKSIDELEMAIEYDIGCIVADNFYEIELINSILQRKNKAMNVLMR 156
                                           ************************************************************************* PP

                             TIGR01048 148 vnpdvdaktheyisTGlkesKFGieve..eaeeayelalkleslelvGihvHIGSqildlepfveaaekvvkl 218
                                           v+p+++++th+yi TG ++sKFG++++  +a ea+ +  ++e+++  G+h HIGSq++++e++  aa+ +++ 
  NCBI__GCF_000224785.1:WP_010530863.1 157 VTPGIEPNTHDYIVTGNEDSKFGFNLAngQADEAFLQLQRSEHIQFKGLHSHIGSQLFETEEILLAAKVLFQK 229
                                           *************************99899******************************************* PP

                             TIGR01048 219 leelkee.gieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klklilEpGRslvanagv 288
                                           l+e++e+  ++ e+l+lGGG+gi+y++e++++d +  ++ l   ++++a   +l  +++++EpGR++++nag+
  NCBI__GCF_000224785.1:WP_010530863.1 230 LAEWHEKyDYTPEVLNLGGGFGIRYTQEDKPLDYSVHVKELSVVVQEQAaYFNLpLPEIWIEPGRAIAGNAGI 302
                                           ****99999*******************************9999999996777789***************** PP

                             TIGR01048 289 lltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelp 360
                                           +l++V+s+Ke +  r++v+vD+gm+d+iRpalY+a++e +++++  +  t tv+++G++CEsgD+l++d  +p
  NCBI__GCF_000224785.1:WP_010530863.1 303 TLYTVGSIKEIPGvRHYVAVDGGMTDNIRPALYNAKYEGVLANKAAQPVTDTVSIAGKCCESGDMLMWDLPVP 375
                                           **********9877*********************************************************** PP

                             TIGR01048 361 eveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                           +ve+ d+lav+s+GAYg+sm+++Yn+ +++a+v+ve+g+ +l+++re+++d+++++
  NCBI__GCF_000224785.1:WP_010530863.1 376 AVESNDILAVFSTGAYGYSMANHYNRFAKAAVVFVENGRDHLVVQRESYQDVVKND 431
                                           ****************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (435 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: 25.11
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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