GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ramA in Clostridium kluyveri DSM 555

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_011989278.1 CKL_RS03490 ASKHA domain-containing protein

Query= reanno::Phaeo:GFF1501
         (698 letters)



>NCBI__GCF_000016505.1:WP_011989278.1
          Length = 647

 Score =  452 bits (1163), Expect = e-131
 Identities = 245/651 (37%), Positives = 388/651 (59%), Gaps = 15/651 (2%)

Query: 23  VVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHGVTVAD 82
           V+F P+G RG+   G  +L A ++ G++L+S CGG G C KC++       +K     ++
Sbjct: 5   VIFQPTGYRGKICSGKTILEACQKFGINLESPCGGNGTCGKCKVKLEKILCNKES-DFSN 63

Query: 83  DALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEARDIT 142
            +++   + E+    K   +   RL C  ++  D+VI VP +S+  +Q + + + ++   
Sbjct: 64  SSISPITEKEREILTKEEQLQNFRLACCTKITEDMVIFVPEKSEKGKQRILETSGSKLFH 123

Query: 143 MNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDL--KGVKTDLHILSVLQPALRKGG 200
           +NP  + YY+E++ P +     D  R+ +AL  ++    K +  D  ++  L   LRK  
Sbjct: 124 LNPGVKKYYIELKSPTLEDCRDDFTRVKDALLHKYRNLEKHISMDYKVMQTLSSLLRKEK 183

Query: 201 WKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVASSGI 260
           +K+TV + +  E     I+ + PGF E +IYG+A+D+G+TTIAA LCDL +G+V+  +  
Sbjct: 184 YKITVTLWMDKE-----IISVEPGFNE-NIYGVAMDVGTTTIAAALCDLSSGEVITQTSS 237

Query: 261 MNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVFV 320
           +NPQI +GED++SR+S+  +NK G +EM   + + +N L  ++AA    +   I D V V
Sbjct: 238 LNPQIIYGEDILSRISHCSINKNGLEEMHSLIIKEINKLLEELAASINRNVNQIYDMVIV 297

Query: 321 CNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGAD 380
            N  MHH+ L I+P  LGQ+PF    S  L ++A ELD+NI   A +Y LP   G VG+D
Sbjct: 298 FNTAMHHIALNINPEYLGQSPFTPVISQGLNIKARELDINICKGAYMYSLPIEGGFVGSD 357

Query: 381 AAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAAP 440
             +V +S+   K + +++++D+GTN EI  GN++ V + S  TGPA EGAQ+  G RA  
Sbjct: 358 NVSVLISQEIHKQDKMLMIIDIGTNGEIDFGNREGVFSTSCATGPALEGAQMKYGMRAVT 417

Query: 441 GAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEMRMAGL 500
           GAIERV+IN  + E  F+VIG D W++           G+ GICGSGII+A+AEM    +
Sbjct: 418 GAIERVKINSLSLEADFKVIGEDKWNN------TAEVGGVKGICGSGIIDAVAEMYKNSI 471

Query: 501 LDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKAALYSG 560
           +   G           R  ++GR    L+W      G  I++T  D+RA+Q+AK+ALY+G
Sbjct: 472 IGKDGTFNKKIVCPRIRRDEEGRMEYVLVWRRHTSIGEDISITQKDVRAVQLAKSALYAG 531

Query: 561 ARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIAL 620
           A++LM K  +D+V+ V+LAGAFG++I+ ++A+V+G+ PDC L+ V   GNAAG GA+IAL
Sbjct: 532 AKMLMKKRNVDSVEGVILAGAFGSYINKENALVIGLFPDCDLNNVVVVGNAAGEGAKIAL 591

Query: 621 LNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIV 671
           L+T+ R+E E   + ++ +E A E  F+  F NA   P+S + FP +  I+
Sbjct: 592 LSTDKRTEAEEVAKDVQFMECAAEKDFEMEFYNAMNFPHSEDEFPHIKHIL 642


Lambda     K      H
   0.318    0.135    0.396 

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: 930
Number of extensions: 46
Number of successful extensions: 5
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: 698
Length of database: 647
Length adjustment: 39
Effective length of query: 659
Effective length of database: 608
Effective search space:   400672
Effective search space used:   400672
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: 54 (25.4 bits)

Align candidate WP_011989278.1 CKL_RS03490 (ASKHA domain-containing protein)
to HMM PF14574 (RACo_C_ter)

# 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/PF14574.10.hmm
# target sequence database:        /tmp/gapView.3083115.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       RACo_C_ter  [M=261]
Accession:   PF14574.10
Description: C-terminal domain of RACo the ASKHA domain
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-97  310.0   2.1    9.8e-97  309.1   2.1    1.5  1  NCBI__GCF_000016505.1:WP_011989278.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016505.1:WP_011989278.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.1   2.1   9.8e-97   9.8e-97       2     260 ..     373     638 ..     372     639 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.1 bits;  conditional E-value: 9.8e-97
                            RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek.... 70 
                                           + ++iDiGTN+Ei +gn++ ++++s+a+GPAlEG+++k+GmrA +gAierv+i++ +le ++kvig++k    
  NCBI__GCF_000016505.1:WP_011989278.1 373 MLMIIDIGTNGEIDFGNREGVFSTSCATGPALEGAQMKYGMRAVTGAIERVKINSLSLEADFKVIGEDKwnnt 445
                                           789****************************************************************999*** PP

                            RACo_C_ter  71 .....pkGicGsGiidliaelleagiidkkgklnkelkserireee.eteeyvlvlaeesetekdivitekDi 137
                                                +kGicGsGiid++ae++++ ii k+g++nk++  +rir++e +++eyvlv+++++++++di+it+kD+
  NCBI__GCF_000016505.1:WP_011989278.1 446 aevggVKGICGSGIIDAVAEMYKNSIIGKDGTFNKKIVCPRIRRDEeGRMEYVLVWRRHTSIGEDISITQKDV 518
                                           *******************************************976599************************ PP

                            RACo_C_ter 138 delirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAra 210
                                           ++++ ak+A+yag+k+L+++ +  v++++ v+laGafGsyi+ e+A++iGl+Pd++l++v+ vGN++++gA++
  NCBI__GCF_000016505.1:WP_011989278.1 519 RAVQLAKSALYAGAKMLMKKRN--VDSVEGVILAGAFGSYINKENALVIGLFPDCDLNNVVVVGNAAGEGAKI 589
                                           ********************99..9************************************************ PP

                            RACo_C_ter 211 allsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsv 260
                                           alls+++r+e+ee+a++++ +e+a+ek+F+ ef +a+ +ph++   fp++
  NCBI__GCF_000016505.1:WP_011989278.1 590 ALLSTDKRTEAEEVAKDVQFMECAAEKDFEMEFYNAMNFPHSED-EFPHI 638
                                           *****************************************877.69986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (647 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: 00:00:00.00
# Mc/sec: 26.31
//
[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:

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