GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Lacinutrix algicola AKS293

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_055435891.1 ASC41_RS06840 diaminopimelate decarboxylase

Query= reanno::Cola:Echvi_1295
         (410 letters)



>NCBI__GCF_001418085.1:WP_055435891.1
          Length = 408

 Score =  476 bits (1226), Expect = e-139
 Identities = 235/397 (59%), Positives = 300/397 (75%), Gaps = 2/397 (0%)

Query: 15  LLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVN-LKIKYATKALSNINILKLMKKAGT 73
           LL IA ++ +PVYVY+ + I  Q   L +AF+ V  +K+ YA KALSNI+ILKLMK  G 
Sbjct: 6   LLKIAKDFESPVYVYNSEIITQQYKRLTSAFNKVKKVKVNYAVKALSNISILKLMKTLGA 65

Query: 74  GVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINIDNIPMLEHFGTYY 133
           G+D VSI+EV+L +  GY+  +I+FTPN V+ EEI+ A  LG  INIDN+ +LE FGT +
Sbjct: 66  GLDTVSIQEVQLGIAAGYKAEQIIFTPNGVSLEEIENAAKLGCQINIDNLSILEQFGTKH 125

Query: 134 GNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEVHNLKVAGLHVHTG 193
            N +P+CIR+NPH++AGGN  ISVGHIDSKFGISI Q+ H+L+IVE  N+ + G+H+HTG
Sbjct: 126 PN-IPVCIRINPHVMAGGNTNISVGHIDSKFGISIHQIPHILRIVENTNMNINGIHMHTG 184

Query: 194 SDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTDMVEVGRKVSAAFK 253
           SDILD +VFL  +EILF+ AK FK+L F+DFG GFKV YK GDI T++ E G K+S  F 
Sbjct: 185 SDILDIDVFLYASEILFETAKNFKNLDFIDFGSGFKVPYKPGDIETNIEEFGEKLSVRFN 244

Query: 254 EFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDSGLNHLIRPMMYDA 313
           EFCK+YG+EL + FEPGKFLVSE G  L   NVVK T ++ F  +DSG NHLIRPM+Y +
Sbjct: 245 EFCKDYGKELILAFEPGKFLVSEAGQFLAKVNVVKQTTSTVFAQIDSGFNHLIRPMLYGS 304

Query: 314 YHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIKNAGAYGFSMASNY 373
            H +ENIS   G +R Y++VGYICETDT A +R++ E+ EGD+L  KNAGAY +SMASNY
Sbjct: 305 QHEIENISNPKGRERFYSVVGYICETDTFANNRRISEINEGDILTFKNAGAYCYSMASNY 364

Query: 374 NSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDIGL 410
           NSR RPAEVL  +G+AHLIR RE+F+DIL +QI I L
Sbjct: 365 NSRYRPAEVLWHNGEAHLIRKRETFDDILNNQIQIDL 401


Lambda     K      H
   0.320    0.139    0.403 

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: 561
Number of extensions: 14
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: 410
Length of database: 408
Length adjustment: 31
Effective length of query: 379
Effective length of database: 377
Effective search space:   142883
Effective search space used:   142883
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_055435891.1 ASC41_RS06840 (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.3737147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-118  380.7   0.1   3.8e-118  380.5   0.1    1.0  1  NCBI__GCF_001418085.1:WP_055435891.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055435891.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.5   0.1  3.8e-118  3.8e-118      13     416 ..       3     396 ..       1     397 [. 0.96

  Alignments for each domain:
  == domain 1  score: 380.5 bits;  conditional E-value: 3.8e-118
                             TIGR01048  13 gvdlkelaeefgtPlYvydeetlrerlealkeafkaees.lvlYAvKAnsnlavlrllaeeGlgldvvsgGEl 84 
                                           +++l ++a+ f +P+Yvy++e +++++++l++af++ ++ +v YAvKA sn+++l+l++ +G+gld vs  E+
  NCBI__GCF_001418085.1:WP_055435891.1   3 NTQLLKIAKDFESPVYVYNSEIITQQYKRLTSAFNKVKKvKVNYAVKALSNISILKLMKTLGAGLDTVSIQEV 75 
                                           678999*****************************96666********************************* PP

                             TIGR01048  85 eralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157
                                           +   aAg+kae+i+f+ ng+s ee+e+a++l+++ in+d+++ le++ +  ++     +v++R+np+v a   
  NCBI__GCF_001418085.1:WP_055435891.1  76 QLGIAAGYKAEQIIFTPNGVSLEEIENAAKLGCQ-INIDNLSILEQFGTKHPNI----PVCIRINPHVMAGGN 143
                                           *********************************9.*****99999996655555....*************** PP

                             TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegiele 230
                                             is G+ +sKFGi+++ + + + +++++ ++++ Gih+H GS ild++ f  a e +++++++      +l 
  NCBI__GCF_001418085.1:WP_055435891.1 144 TNISVGHIDSKFGISIH-QIPHILRIVENTNMNINGIHMHTGSDILDIDVFLYASEILFETAKN----FKNLD 211
                                           *****************.7778888888899*******************************99....5799* PP

                             TIGR01048 231 eldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesr 302
                                           ++d+G G+ ++y++ + + ++ee+ ekl  ++++ + ++g++l l +EpG++lv++ag +l++V++vK++ s+
  NCBI__GCF_001418085.1:WP_055435891.1 212 FIDFGSGFKVPYKPGDIETNIEEFGEKLSVRFNEFCkDYGKELILAFEPGKFLVSEAGQFLAKVNVVKQTTST 284
                                           ************************************9************************************ PP

                             TIGR01048 303 kfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGA 375
                                            f+ +D+g+n liRp+lY+++hei ++++ + + +  ++vvG +CE+ D++a++r+++e++eGd+l  ++aGA
  NCBI__GCF_001418085.1:WP_055435891.1 285 VFAQIDSGFNHLIRPMLYGSQHEIENISNPKGR-ERFYSVVGYICET-DTFANNRRISEINEGDILTFKNAGA 355
                                           ***************************887766.899*********7.************************* PP

                             TIGR01048 376 YgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                           Y++sm+snYnsr rpaevl+++g+a+lir+ret++d+l+++
  NCBI__GCF_001418085.1:WP_055435891.1 356 YCYSMASNYNSRYRPAEVLWHNGEAHLIRKRETFDDILNNQ 396
                                           **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (408 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: 17.53
//
[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