Alignments for a candidate for ramA in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfatibacillum aliphaticivorans DSM 15576

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_028314329.1 G491_RS0108760 DUF4445 domain-containing protein

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



>NCBI__GCF_000429905.1:WP_028314329.1
          Length = 610

 Score =  305 bits (781), Expect = 4e-87
 Identities = 207/641 (32%), Positives = 317/641 (49%), Gaps = 53/641 (8%)

Query: 23  VVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHGVTVAD 82
           V F P G+R   P  T +  AA+  GV L + CGG+G C KC++    G     G    D
Sbjct: 11  VEFQPLGRRIEAPFETTIAQAAQSAGVPLAADCGGKGKCGKCRVHILAG-----GAAPPD 65

Query: 83  DALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEARDIT 142
            +       E +  ++       RL C  ++ GDV I VP  S VH Q ++     R   
Sbjct: 66  SS-------ELKVLEQSSAAPQERLACMTRILGDVKIHVPKASMVHEQSLQLEGRMRSPD 118

Query: 143 MNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPALRKGGWK 202
            +   +  +V +  P++     D  RL EA+DA WD  G       +  L  +LR+   +
Sbjct: 119 GDRLVQSRFVNLPLPNLQDQRSDSRRLSEAMDA-WDENGWTLSPEFVRRLSGSLRESNGE 177

Query: 203 VTVAVHLGDENHPPKIMHIWPGFYEG--SIYGLAVDLGSTTIAAHLCDLKTGDVVASSGI 260
           +TV +  G             G   G  +  G A DLG+TTIA  L DL+TG+++ S G 
Sbjct: 178 LTVFLQDGAPI----------GLIAGKKTPIGAAFDLGTTTIAGRLVDLETGEILCSEGC 227

Query: 261 MNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVFV 320
           MNPQI +GED++SR+ Y++ N  G   ++ A ++ +N L + +   A ++   + +    
Sbjct: 228 MNPQISYGEDVISRLDYAIHNPDGPGRLSAAAKDAINDLLSALCKNAGVEPERVSNISVA 287

Query: 321 CNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGAD 380
           CN  M HL L +    L ++P+A   SN L L      +   P A+VY+ PCI G VG D
Sbjct: 288 CNTAMSHLLLKLPASPLARSPYAAGFSNPLELTGKAFGIKDAPTAKVYVFPCIEGFVGGD 347

Query: 381 AAAVALSEAPDKSEDLVLVVDVGTNAEILL---GNKDKVLACSSPTGPAFEGAQISSGQR 437
             A+ L+   D++++  L VD+GTN EI+L   G    +   S  +GPA EGA +  G R
Sbjct: 348 HTAMILACGLDQADETCLGVDIGTNTEIVLTRPGADGGMFVTSCASGPALEGAHVRDGMR 407

Query: 438 AAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEMRM 497
           A+PGAI +V I            G +I++        +      GICGSG+++A+AEM  
Sbjct: 408 ASPGAIHKVRITEN---------GPEIFT--------INNEPPVGICGSGLVDALAEMVR 450

Query: 498 AGLLDASGLIGSAEQTGTTRCIQDGRTNAYLL-WDGSVEGGPTITVTNPDIRAIQMAKAA 556
           AG+LD+ G   + E  G  +     R   YLL      +    I +T  DI  +Q+AK A
Sbjct: 451 AGVLDSRGHF-TYEAKGVHK---SPRGKYYLLATKEKDQAKQDIIITQKDISELQLAKGA 506

Query: 557 LYSGARLLMDKFGIDT--VDRVVLAGAFGAHISAKHAMVLGMIPDCPLD-KVTSAGNAAG 613
           +++G + L+ + GI    + RV +AGAFG+H++ + A+ + ++P+   D +   AGNAA 
Sbjct: 507 IHAGVQKLLQQMGISAKEISRVYMAGAFGSHLNMESALAIRLLPEDLADAEFVQAGNAAA 566

Query: 614 TGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNA 654
            GA +ALL+   RS  E   +    +E A +  F    V A
Sbjct: 567 DGACLALLSRRERSRAEKIARNAVHVEMANDSSFSSVLVKA 607


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: 906
Number of extensions: 42
Number of successful extensions: 7
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: 610
Length adjustment: 38
Effective length of query: 660
Effective length of database: 572
Effective search space:   377520
Effective search space used:   377520
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_028314329.1 G491_RS0108760 (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.13658.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      3e-82  261.6   0.6    8.9e-81  256.8   0.6    2.1  2  lcl|NCBI__GCF_000429905.1:WP_028314329.1  G491_RS0108760 DUF4445 domain-co


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028314329.1  G491_RS0108760 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.0    0.0028    0.0028     142     171 ..     258     287 ..     216     293 .. 0.94
   2 !  256.8   0.6   8.9e-81   8.9e-81       1     248 [.     362     609 ..     362     610 .] 0.96

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0028
                                RACo_C_ter 142 rakaAiyagvktLleevglevedidkvyla 171
                                                ak Ai+  ++ L++++g+e e+++++ +a
  lcl|NCBI__GCF_000429905.1:WP_028314329.1 258 AAKDAINDLLSALCKNAGVEPERVSNISVA 287
                                               6999***********************998 PP

  == domain 2  score: 256.8 bits;  conditional E-value: 8.9e-81
                                RACo_C_ter   1 eislliDiGTNaEivl...gnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvi 66 
                                               e++l +DiGTN Eivl   g +  ++++s+a+GPAlEG++++ GmrA+pgAi++v+i+++   +e+ +i
  lcl|NCBI__GCF_000429905.1:WP_028314329.1 362 ETCLGVDIGTNTEIVLtrpGADGGMFVTSCASGPALEGAHVRDGMRASPGAIHKVRITENG--PEIFTI 428
                                               6899************44446789************************************9..****** PP

                                RACo_C_ter  67 gnekpkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitek 135
                                               +ne+p+GicGsG++d++ae+++ag++d++g+++ e   + ++++ + + y+l+++e+ + ++di+it+k
  lcl|NCBI__GCF_000429905.1:WP_028314329.1 429 NNEPPVGICGSGLVDALAEMVRAGVLDSRGHFTYE--AKGVHKSPRGKYYLLATKEKDQAKQDIIITQK 495
                                               ********************************665..78999999************************ PP

                                RACo_C_ter 136 DidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPd.lelekvkqvGNt 203
                                               Di+el+ ak+Ai+agv+ Ll+++g+++++i++vy+aGafGs++++e+A+ i llP+ l+ ++++q+GN+
  lcl|NCBI__GCF_000429905.1:WP_028314329.1 496 DISELQLAKGAIHAGVQKLLQQMGISAKEISRVYMAGAFGSHLNMESALAIRLLPEdLADAEFVQAGNA 564
                                               *******************************************************7588999******* PP

                                RACo_C_ter 204 slagAraallsreareeleeiarkityielavekkFmeefvaalf 248
                                               +  gA  allsr++r+++e+iar+  ++e+a++++F +  v+a+ 
  lcl|NCBI__GCF_000429905.1:WP_028314329.1 565 AADGACLALLSRRERSRAEKIARNAVHVEMANDSSFSSVLVKAMR 609
                                               *****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (610 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: 16.56
//
[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