Alignments for a candidate for ramA in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfotomaculum ruminis DSM 2154

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_013841548.1 DESRU_RS07710 DUF4445 domain-containing protein

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



>NCBI__GCF_000215085.1:WP_013841548.1
          Length = 614

 Score =  289 bits (739), Expect = 3e-82
 Identities = 201/642 (31%), Positives = 315/642 (49%), Gaps = 45/642 (7%)

Query: 23  VVFTPSGKRGRFPVGTPVLTAARQLG---VDLDSVCGGRGICSKCQITPSYGEFSKHGVT 79
           V F P+    +   G  +L  AR+ G   V+L S CGG+G+C  C+            V 
Sbjct: 6   VGFKPADCIIQIEAGKTILDVAREFGLSAVNLASPCGGQGLCGCCR------------VK 53

Query: 80  VADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEAR 139
           V  D  ++  K E +      L  G RL CQA+V G   +++ P++    Q +  +    
Sbjct: 54  VTGDHFSQRTKAEIKSLLPEELAQGYRLACQARVWGPGEVEISPQAAGEVQFLEIQGLIL 113

Query: 140 DITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPALRKG 199
            +  NP    Y +E+E+          + +   L  Q+DL  +K D  +     P     
Sbjct: 114 AVQPNPPVASYTIELEKGSWPCSQLAWQEIKNCLATQYDLGRLKIDPELYREKCPVKLTK 173

Query: 200 GWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVASSG 259
              VTV           +I++ + G       GLAVDLG+T IA +L +L++G V+A   
Sbjct: 174 EAVVTVRER--------EIINCFFGSSPSPPVGLAVDLGTTKIAGYLINLESGVVLAGGT 225

Query: 260 IMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVF 319
           I+NPQ  +G DLMSR+SY++ ++   + + R V + +N L   +A +A +    IV+AV 
Sbjct: 226 IVNPQRVYGYDLMSRLSYALESEAKYRRLNRDVIDSINHLAANLAGQAGLGVKDIVEAVV 285

Query: 320 VCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGA 379
             N  MHHLFL +   +L +AP+    + ++ ++A E+ L I P A VY+LP +AG VG 
Sbjct: 286 AGNTAMHHLFLRLPVDQLSRAPYLPVVTTSVEIKAREIGLVISPGAYVYVLPPVAGFVGG 345

Query: 380 DAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAA 439
           D  A+ L    D+++ + L +D+GTN EI+L    ++ +CS  +GPAFEG  I  G +A 
Sbjct: 346 DHVAMILGSQLDRTDKVSLGLDIGTNTEIVLCYGGRMRSCSCASGPAFEGTHIRHGVQAV 405

Query: 440 PGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEMRMAG 499
            GAI  V +  +  E +   +G                T   GICGSGI++A+AE+   G
Sbjct: 406 RGAIRSVRLGRDGLEAQLETVGD---------------TAPLGICGSGILDAVAELYRTG 450

Query: 500 LLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEG-GPTITVTNPDIRAIQMAKAALY 558
           ++   G +  +      R  + G    Y L   S  G G  + +T  DI  I +AKAA+ 
Sbjct: 451 VITRQGRLNRSHP--RVRLSEMGL--QYTLVPASKSGTGKELVITQQDIEEIMLAKAAIA 506

Query: 559 SGARLLMDKFGIDTVD--RVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGA 616
           +G RL++    +   D   VV+AGAFG  +    AMV+GM P+   +     GNAAG G+
Sbjct: 507 TGIRLMLQAVDLTCKDIQEVVVAGAFGTQLKVTSAMVVGMFPNLSQELFRQVGNAAGAGS 566

Query: 617 RIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIP 658
           +  L++   R   E     IE +E +    FQE + ++  +P
Sbjct: 567 QAVLVSLAERRRAEKIAAVIEHLELSTMSSFQEVYFSSLTLP 608


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: 842
Number of extensions: 37
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: 614
Length adjustment: 38
Effective length of query: 660
Effective length of database: 576
Effective search space:   380160
Effective search space used:   380160
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_013841548.1 DESRU_RS07710 (DUF4445 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.24020.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.6e-85  271.7   0.3    2.6e-85  271.7   0.3    1.7  2  lcl|NCBI__GCF_000215085.1:WP_013841548.1  DESRU_RS07710 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013841548.1  DESRU_RS07710 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1     0.093     0.093     152     174 ..     267     289 ..     260     292 .. 0.81
   2 !  271.7   0.3   2.6e-85   2.6e-85       2     251 ..     362     609 ..     361     613 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.093
                                RACo_C_ter 152 ktLleevglevedidkvylaGaf 174
                                               + L  ++gl v+di + ++aG +
  lcl|NCBI__GCF_000215085.1:WP_013841548.1 267 ANLAGQAGLGVKDIVEAVVAGNT 289
                                               56788999999***999999975 PP

  == domain 2  score: 271.7 bits;  conditional E-value: 2.6e-85
                                RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek 70 
                                               +sl +DiGTN Eivl    ++ ++s+a+GPA+EG +i++G++A +gAi +v++ ++ le +l+++g+++
  lcl|NCBI__GCF_000215085.1:WP_013841548.1 362 VSLGLDIGTNTEIVLCYGGRMRSCSCASGPAFEGTHIRHGVQAVRGAIRSVRLGRDGLEAQLETVGDTA 430
                                               78999**************************************************************** PP

                                RACo_C_ter  71 pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitekDide 139
                                               p GicGsGi+d++ael+++g+i+++g+ln++  ++r+r +e   +y+lv+a++s+t+k++vit++Di+e
  lcl|NCBI__GCF_000215085.1:WP_013841548.1 431 PLGICGSGILDAVAELYRTGVITRQGRLNRS--HPRVRLSEMGLQYTLVPASKSGTGKELVITQQDIEE 497
                                               ****************************886..9*********************************** PP

                                RACo_C_ter 140 lirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagA 208
                                               ++ akaAi +g++++l++v+l+++di++v++aGafG+ +++++A+++G++P+l++e ++qvGN+++ag+
  lcl|NCBI__GCF_000215085.1:WP_013841548.1 498 IMLAKAAIATGIRLMLQAVDLTCKDIQEVVVAGAFGTQLKVTSAMVVGMFPNLSQELFRQVGNAAGAGS 566
                                               ********************************************************************* PP

                                RACo_C_ter 209 raallsreareeleeiarkityielavekkFmeefvaalflph 251
                                               +a+l+s ++r+++e+ia  i+++el++ ++F+e ++++l lp 
  lcl|NCBI__GCF_000215085.1:WP_013841548.1 567 QAVLVSLAERRRAEKIAAVIEHLELSTMSSFQEVYFSSLTLPP 609
                                               ***************************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (614 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: 18.42
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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