GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Flavobacterium glycines Gm-149

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_066324151.1 BLR17_RS08045 diaminopimelate decarboxylase

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



>NCBI__GCF_900100165.1:WP_066324151.1
          Length = 405

 Score =  488 bits (1257), Expect = e-142
 Identities = 236/400 (59%), Positives = 309/400 (77%), Gaps = 2/400 (0%)

Query: 10  VQGVPLLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVN-LKIKYATKALSNINILKLM 68
           +Q   LL +A ++G+P+YVYD +KI  Q   L  AFS V  L+I YA KALSN+ IL+L+
Sbjct: 1   MQSKDLLQLAEQFGSPLYVYDAEKIKSQYNRLTKAFSKVEKLRINYAMKALSNVAILQLL 60

Query: 69  KKAGTGVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINIDNIPMLEH 128
           ++ G+ +DAVSI+EV+L LH GY P +I FTPN V+ EEI+E   LGV INIDN+ +LE 
Sbjct: 61  RELGSCLDAVSIQEVQLGLHAGYSPDQIFFTPNGVSLEEIEEVHSLGVQINIDNLSILEQ 120

Query: 129 FGTYYGNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEVHNLKVAGL 188
           FG  + + VP+CIR+NPH++AGGN  ISVGHIDSKFGIS+ QL H+++IVE  N+ +AG+
Sbjct: 121 FGAKHPH-VPVCIRINPHVMAGGNENISVGHIDSKFGISVHQLPHLVRIVENTNMNIAGI 179

Query: 189 HVHTGSDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTDMVEVGRKV 248
           H+HTGSDILD EVFL  AEILFDAAK FK+L+FLDFG GFKV YK+ DI TD+ E+G+K+
Sbjct: 180 HMHTGSDILDIEVFLYAAEILFDAAKNFKNLEFLDFGSGFKVPYKKDDIETDIEELGKKL 239

Query: 249 SAAFKEFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDSGLNHLIRP 308
           S  F  FC  YG+EL + FEPGKFLVSE G+ L   NVVK T ++ F G+DSG NHLIRP
Sbjct: 240 SKRFNAFCDEYGKELTLIFEPGKFLVSEAGFFLAKVNVVKQTTSTVFAGIDSGFNHLIRP 299

Query: 309 MMYDAYHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIKNAGAYGFS 368
           M Y + H +ENIS   G +R Y++VGYICETDT A++R+++E+ EGD+L  +NAGAY +S
Sbjct: 300 MFYGSQHHIENISNPKGKERFYSVVGYICETDTFASNRRIQEIAEGDILCFRNAGAYCYS 359

Query: 369 MASNYNSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDI 408
           M+SNYNSR +PAEVL ++G+ HLIRA E+FED+L++QI +
Sbjct: 360 MSSNYNSRYKPAEVLWINGEGHLIRAHETFEDLLKNQIPL 399


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: 559
Number of extensions: 23
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: 405
Length adjustment: 31
Effective length of query: 379
Effective length of database: 374
Effective search space:   141746
Effective search space used:   141746
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_066324151.1 BLR17_RS08045 (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.4036780.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-121  389.4   0.0   8.8e-121  389.2   0.0    1.0  1  NCBI__GCF_900100165.1:WP_066324151.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066324151.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.2   0.0  8.8e-121  8.8e-121      13     416 ..       3     396 ..       1     397 [. 0.95

  Alignments for each domain:
  == domain 1  score: 389.2 bits;  conditional E-value: 8.8e-121
                             TIGR01048  13 gvdlkelaeefgtPlYvydeetlrerlealkeafkaees.lvlYAvKAnsnlavlrllaeeGlgldvvsgGEl 84 
                                             dl +lae+fg+PlYvyd+e++++++++l++af++ e+ ++ YA+KA sn+a+l+ll+e+G++ld+vs  E+
  NCBI__GCF_900100165.1:WP_066324151.1   3 SKDLLQLAEQFGSPLYVYDAEKIKSQYNRLTKAFSKVEKlRINYAMKALSNVAILQLLRELGSCLDAVSIQEV 75 
                                           56899*******************************6666********************************* PP

                             TIGR01048  85 eralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157
                                           +  l+Ag+++++i f+ ng+s ee+e++ +l+++ in+d+++ le++ +  +    +++v++R+np+v a   
  NCBI__GCF_900100165.1:WP_066324151.1  76 QLGLHAGYSPDQIFFTPNGVSLEEIEEVHSLGVQ-INIDNLSILEQFGAKHP----HVPVCIRINPHVMAGGN 143
                                           *********************************9.****9999998854444....56*************** PP

                             TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegiele 230
                                           e is G+ +sKFGi+v++  + ++ ++++ ++++ Gih+H GS ild+e f  aae +++++++      +le
  NCBI__GCF_900100165.1:WP_066324151.1 144 ENISVGHIDSKFGISVHQLPHLVR-IVENTNMNIAGIHMHTGSDILDIEVFLYAAEILFDAAKN----FKNLE 211
                                           *****************6655555.556677*******************************99....589** PP

                             TIGR01048 231 eldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesr 302
                                           +ld+G G+ ++y++++ + d+ee+ +kl ++++  + e+g++l+li+EpG++lv++ag +l++V++vK++ s+
  NCBI__GCF_900100165.1:WP_066324151.1 212 FLDFGSGFKVPYKKDDIETDIEELGKKLSKRFNAFCdEYGKELTLIFEPGKFLVSEAGFFLAKVNVVKQTTST 284
                                           ************************************9************************************ PP

                             TIGR01048 303 kfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGA 375
                                            f+ +D+g+n liRp+ Y+++h+i ++++ + + +  ++vvG +CE+ D++a +r+++e+ eGd+l  ++aGA
  NCBI__GCF_900100165.1:WP_066324151.1 285 VFAGIDSGFNHLIRPMFYGSQHHIENISNPKGK-ERFYSVVGYICET-DTFASNRRIQEIAEGDILCFRNAGA 355
                                           ***************************886665.899*********7.************************* PP

                             TIGR01048 376 YgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                           Y++smssnYnsr +paevl+ +g+ +lir  et+edll+++
  NCBI__GCF_900100165.1:WP_066324151.1 356 YCYSMSSNYNSRYKPAEVLWINGEGHLIRAHETFEDLLKNQ 396
                                           **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.44
//
[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