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_013841581.1 DESRU_RS07880 DUF4445 domain-containing protein

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



>NCBI__GCF_000215085.1:WP_013841581.1
          Length = 541

 Score =  208 bits (529), Expect = 6e-58
 Identities = 142/438 (32%), Positives = 223/438 (50%), Gaps = 37/438 (8%)

Query: 232 GLAVDLGSTTIAAHLCDLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRA 291
           G+AVDLG+TTI  +L DL +G  +    ++N Q  +G D++SR+++++      +E+  A
Sbjct: 124 GMAVDLGTTTIVGYLYDLYSGRRLGVMPVVNGQRIYGADVISRLAHAIKGPDAYRELRGA 183

Query: 292 VREGMNALFTQIAAEAEIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALA 351
           V + +N LF     +  +    + + V V NP M HL L +    L   PF         
Sbjct: 184 VLQDLNQLFLGCCEQGGVSPRFLREIVLVGNPAMMHLVLNLPVESLAAVPFCPYEPGPFY 243

Query: 352 LRAVELDLNIHPAARVYLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLG 411
             A EL L     A  Y  P I G VG+DA A A      + ++ +L+VD+GTN EILL 
Sbjct: 244 RTAEELGLESVSRAICYFPPFIGGFVGSDALAAAQVHGFGERQETLLLVDIGTNGEILLQ 303

Query: 412 NKDKVLACSSPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGF 471
             +++LA S+P GPA EG  I+ G+ A  GAI +V +                  D D  
Sbjct: 304 FGEQLLAASAPAGPALEGGNIACGKTAVTGAIHKVTM------------------DYDVH 345

Query: 472 AAAVATTGITGICGSGIIEAIAEMRMAG-------LLDASGLIGSAEQTGTTRCI--QDG 522
              + +   TGICGSG+++A+AEM   G       L+ ASGL          R +   DG
Sbjct: 346 LEVIGSAKPTGICGSGLVDAVAEMLRLGIIKSDGELVKASGLPPITSYKIKQRLVTGADG 405

Query: 523 RTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKAALYSGARLLMDKFGI--DTVDRVVLAG 580
             N  +L D        + +   DIR IQ+AK A+ +G ++LMD+ GI    ++ ++LAG
Sbjct: 406 -LNQLMLTD-------KLYLHQKDIREIQLAKGAVAAGIQVLMDEAGIGEKELNSLLLAG 457

Query: 581 AFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIALLNTEARSEIEATVQQIEKIE 640
            FG +++  +A+ +G++   PL K+   GNAAG+GA + LL+   R   E    + + +E
Sbjct: 458 GFGNYLNPANALRMGLLGLAPLHKIRQVGNAAGSGACMILLSYPERQRAEKLSLRFKHLE 517

Query: 641 TAVEPRFQEHFVNASAIP 658
            A + R+++ F++    P
Sbjct: 518 LAEDCRYRQQFISQLNFP 535



 Score = 48.9 bits (115), Expect = 6e-10
 Identities = 29/69 (42%), Positives = 33/69 (47%)

Query: 18 ASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHG 77
          AS   V F P       P GT +L AARQ GV L + CGG G C  C+I  + GE     
Sbjct: 3  ASKVRVTFKPHNVEIAVPAGTTILEAARQAGVPLTAPCGGNGRCGGCRIQTASGEEFLAC 62

Query: 78 VTVADDALT 86
           T  D  LT
Sbjct: 63 RTKIDQPLT 71


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: 819
Number of extensions: 40
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 698
Length of database: 541
Length adjustment: 37
Effective length of query: 661
Effective length of database: 504
Effective search space:   333144
Effective search space used:   333144
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: 53 (25.0 bits)

Align candidate WP_013841581.1 DESRU_RS07880 (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.23240.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.5e-77  243.6   0.0    1.6e-76  242.9   0.0    1.3  1  lcl|NCBI__GCF_000215085.1:WP_013841581.1  DESRU_RS07880 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013841581.1  DESRU_RS07880 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.9   0.0   1.6e-76   1.6e-76       1     253 [.     287     538 ..     287     540 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.9 bits;  conditional E-value: 1.6e-76
                                RACo_C_ter   1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvigne 69 
                                               e+ ll+DiGTN+Ei l+  ++llaasa+aGPAlEGg+i cG +A +gAi++v++d +   v+l+vig++
  lcl|NCBI__GCF_000215085.1:WP_013841581.1 287 ETLLLVDIGTNGEILLQFGEQLLAASAPAGPALEGGNIACGKTAVTGAIHKVTMDYD---VHLEVIGSA 352
                                               6789************************************************99877...5******** PP

                                RACo_C_ter  70 kpkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeeset..ekdivitekD 136
                                               kp+GicGsG++d++ae+l+ gii+++g+l k    + i++ + ++++v   +  ++   ++++++++kD
  lcl|NCBI__GCF_000215085.1:WP_013841581.1 353 KPTGICGSGLVDAVAEMLRLGIIKSDGELVKASGLPPITSYKIKQRLVTGADGLNQLmlTDKLYLHQKD 421
                                               *******************************999999998876666666555434333367******** PP

                                RACo_C_ter 137 idelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtsl 205
                                               i+e++ ak+A+ ag+++L++e+g+  +++++++laG+fG+y+++++A+++Gll   +l+k++qvGN+++
  lcl|NCBI__GCF_000215085.1:WP_013841581.1 422 IREIQLAKGAVAAGIQVLMDEAGIGEKELNSLLLAGGFGNYLNPANALRMGLLGLAPLHKIRQVGNAAG 490
                                               ********************************************************************* PP

                                RACo_C_ter 206 agAraallsreareeleeiarkityielavekkFmeefvaalflphtd 253
                                               +gA ++lls  +r+++e+++ + +++ela++ ++ ++f+++l +p+++
  lcl|NCBI__GCF_000215085.1:WP_013841581.1 491 SGACMILLSYPERQRAEKLSLRFKHLELAEDCRYRQQFISQLNFPEKE 538
                                               *********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (541 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: 18.67
//
[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