Alignments for a candidate for ramA in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfacinum hydrothermale DSM 13146

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_084058852.1 B9A12_RS14650 DUF4445 domain-containing protein

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



>NCBI__GCF_900176285.1:WP_084058852.1
          Length = 651

 Score =  304 bits (778), Expect = 1e-86
 Identities = 204/677 (30%), Positives = 334/677 (49%), Gaps = 70/677 (10%)

Query: 23  VVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYG--EFSKHGVTV 80
           V F P  +      G  +L AA Q G+ ++S+CGG G+C KC++    G  E S  GV  
Sbjct: 11  VTFQPENRVVEASPGDTLLDAAAQAGIYINSLCGGEGVCGKCRLKVLSGQVEMSSQGVG- 69

Query: 81  ADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQG-DVVIDVPPESQVHRQVVRK----- 134
                         + D++ L  G  L CQ+ ++  DV + +PPE++   + +       
Sbjct: 70  --------------FLDRKELDAGFVLACQSTLKDQDVEVWIPPEARQEEEQILMVDNIV 115

Query: 135 ---RAEARDITMNPSTRLYY--------VEVEEPDMHKPTGDMERLIEAL-----DAQWD 178
                  ++    P+   YY        +++ EP +     D+ER+  AL     D +W+
Sbjct: 116 HYAEPSPQEAGTVPAPVPYYKPLCDKVFLKLPEPTIQDNLSDLERIYRALARKHPDVKWE 175

Query: 179 LKGVKTDLHILSVLQPALRKGGWKVTVAVHLGDEN-HPPKIMHIWPGFYEGSIYGLAVDL 237
                +D   L  L   LRK  W+VT  VH  D   H  + +   PG      YG+A+D+
Sbjct: 176 -----SDFACLKDLAHLLRKNNWEVTALVHCLDAQCHHVRALE--PGDTSKRTYGVAIDV 228

Query: 238 GSTTIAAHLCDLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMN 297
           G+TTI A L DLKTG V+      N Q R+GED++SR+ ++   +GG   +  AV   +N
Sbjct: 229 GTTTIVAQLVDLKTGKVIGVEASHNQQARYGEDVISRMIFAC-GRGGVDPLKNAVVTTIN 287

Query: 298 ALFTQIAAEAEIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVEL 357
           +L   + A A I    IV  V   N  M HL +G++P  +   P+    +     RA E+
Sbjct: 288 SLIHSLVAGAGIQPTDIVSFVAAGNTTMTHLLVGLEPCTIRVEPYIPTATRIPWARAAEV 347

Query: 358 DLNIHPAARVYLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVL 417
            L  HP A ++ +PC++ +VG D  A  L+   + S  L  ++D+GTN EI++GN + ++
Sbjct: 348 GLTGHPDALLHCMPCVSSYVGGDITAGVLACGMNDSSQLSALIDIGTNGEIVVGNNEWLV 407

Query: 418 ACSSPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVAT 477
            CS+  GPAFEG     G RA  GA+++V I+ +  E   + IG                
Sbjct: 408 CCSASAGPAFEGGGTKCGMRATKGAVQKVRIHGDRVE--IQTIGGG-------------- 451

Query: 478 TGITGICGSGIIEAIAEMRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGG 537
               GICGSG+I+ +AE+   G++D +G   + +       + DG     +  +   E G
Sbjct: 452 -KARGICGSGLIDCMAELVAEGIIDQNGKFIALDHPRVR--VTDGVPEFVVAQESESETG 508

Query: 538 PTITVTNPDIRAIQMAKAALYSGARLLMDKFGID--TVDRVVLAGAFGAHISAKHAMVLG 595
             + +T  DI  +  +KAA+ +  ++L++  G+    +DR+ +AG FGAH+  + ++ +G
Sbjct: 509 EAVVITEDDIGNLMKSKAAVLAAMKILLEGLGLQFFDLDRLYVAGGFGAHLDIEKSIRIG 568

Query: 596 MIPDCPLDKVTSAGNAAGTGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNAS 655
           ++PD P +K+   GN++  GAR ALL+T A  +  A  +Q+   E +V   F   FV A 
Sbjct: 569 LLPDVPKEKILFIGNSSVAGARQALLSTHAYRKANAIARQMTYFELSVHAGFMNEFVAAL 628

Query: 656 AIPNSAEP-FPILSSIV 671
            +P++ E  FP +  ++
Sbjct: 629 FLPHTDESLFPSVRQVL 645


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: 982
Number of extensions: 54
Number of successful extensions: 6
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: 651
Length adjustment: 39
Effective length of query: 659
Effective length of database: 612
Effective search space:   403308
Effective search space used:   403308
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_084058852.1 B9A12_RS14650 (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.15132.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-105  337.4   1.1   8.1e-105  335.6   0.2    2.0  2  lcl|NCBI__GCF_900176285.1:WP_084058852.1  B9A12_RS14650 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084058852.1  B9A12_RS14650 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.019     0.019     146     174 ..     285     313 ..     275     318 .. 0.84
   2 !  335.6   0.2  8.1e-105  8.1e-105       2     260 ..     386     641 ..     385     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.019
                                RACo_C_ter 146 AiyagvktLleevglevedidkvylaGaf 174
                                                i++ ++ L+  +g++ +di +++ aG +
  lcl|NCBI__GCF_900176285.1:WP_084058852.1 285 TINSLIHSLVAGAGIQPTDIVSFVAAGNT 313
                                               5778888899999*************975 PP

  == domain 2  score: 335.6 bits;  conditional E-value: 8.1e-105
                                RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek 70 
                                               +s liDiGTN+Eiv+gn++wl+++sa+aGPA+EGg++kcGmrA++gA+++v+i+ +   ve+++ig+ k
  lcl|NCBI__GCF_900176285.1:WP_084058852.1 386 LSALIDIGTNGEIVVGNNEWLVCCSASAGPAFEGGGTKCGMRATKGAVQKVRIHGDR--VEIQTIGGGK 452
                                               6789**************************************************999..9********* PP

                                RACo_C_ter  71 pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitekDide 139
                                               ++GicGsG+id++ael+ +giid++gk+   l+++r+r +++ +e+v+++++eset++ +vite Di +
  lcl|NCBI__GCF_900176285.1:WP_084058852.1 453 ARGICGSGLIDCMAELVAEGIIDQNGKF-IALDHPRVRVTDGVPEFVVAQESESETGEAVVITEDDIGN 520
                                               ****************************.5579************************************ PP

                                RACo_C_ter 140 lirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagA 208
                                               l+++kaA+ a++k+Lle +gl++ d+d++y+aG+fG+++d+ek+i+iGllPd+++ek+ ++GN+s+agA
  lcl|NCBI__GCF_900176285.1:WP_084058852.1 521 LMKSKAAVLAAMKILLEGLGLQFFDLDRLYVAGGFGAHLDIEKSIRIGLLPDVPKEKILFIGNSSVAGA 589
                                               ********************************************************************* PP

                                RACo_C_ter 209 raallsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsv 260
                                               r+alls++a++++++iar++ty+el+v++ Fm+efvaalflphtd +lfpsv
  lcl|NCBI__GCF_900176285.1:WP_084058852.1 590 RQALLSTHAYRKANAIARQMTYFELSVHAGFMNEFVAALFLPHTDESLFPSV 641
                                               **************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (651 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.91
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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