Alignments for a candidate for ramA in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Ammonifex degensii KC4

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_015738377.1 ADEG_RS01690 DUF4445 domain-containing protein

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



>NCBI__GCF_000024605.1:WP_015738377.1
          Length = 622

 Score =  323 bits (827), Expect = 2e-92
 Identities = 216/651 (33%), Positives = 337/651 (51%), Gaps = 41/651 (6%)

Query: 21  PLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHGVTV 80
           P V F P G     P+G  +L AA + G+ L+  CGG G+C +C+            V V
Sbjct: 2   PRVRFLPEGITVEVPLGNTLLQAAARAGIVLEGACGGEGVCGRCR------------VQV 49

Query: 81  ADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEARD 140
            +  +T         ++++   +G  L CQA  +G+V + VP  S      V K  E+  
Sbjct: 50  QEGKVTSPPNPRLSLQERQ---EGWVLACQAVPEGEVAVFVPESSVFTAHRVLKAEES-- 104

Query: 141 ITMNPSTRLYYVE---VEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPALR 197
           +T+     L++ E   +  P +   T D  RL  AL  Q  +  +    H+L+ L   LR
Sbjct: 105 LTLQTKEPLWWEEKLTLPPPTLEDNTDDWGRLSWALQ-QRGIAPLWPSRHLLAELPRTLR 163

Query: 198 KGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVAS 257
              W+V V +   D+    ++  I P       +G+AVDLG+TT+AA L DL TG VVA+
Sbjct: 164 AADWQVKVELAFLDKALY-ELQGIKPAGRGEGTWGVAVDLGTTTVAAELVDLATGQVVAT 222

Query: 258 SGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDA 317
           +G  N Q  FG+D++SR+ Y+     G +E+ +A+ E +N L  ++  EA I    I   
Sbjct: 223 AGTYNRQAAFGDDVISRIVYATETPRGREELQQAILETVNGLIDELCREAGISFKDIRAV 282

Query: 318 VFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHV 377
           V   N  M HL L +DP  +   P+  A +    ++A +L L  HP A VYL+P +A +V
Sbjct: 283 VGAGNTTMVHLLLNLDPTYIRLEPYVPAANAPPPVKAAKLGLKAHPEAWVYLVPGVASYV 342

Query: 378 GADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQR 437
           G D  A        + E+L L +D+GTN E++LGN++ ++AC+   GPAFEG+ I+ G R
Sbjct: 343 GGDVVAGVKVTGVGEEEELTLFLDIGTNGEMVLGNREWLMACACSAGPAFEGSGITCGMR 402

Query: 438 AAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEMRM 497
           A  GAIE VE++P  +E  +R +        DG           GICGSG+I  ++ +  
Sbjct: 403 AVAGAIEEVEVSPGGEEVFYRTV--------DGKKP-------LGICGSGLISLLSSLLR 447

Query: 498 AGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKAAL 557
           AG++D SG       T   R  ++G+    L+W  S   G  I VT  D++ +  AKAA+
Sbjct: 448 AGVIDRSGRFVEGLDTPRLREGEEGK-EFVLVWGESTGHGRDIYVTQGDLQNLLRAKAAI 506

Query: 558 YSGARLLMDKFGID--TVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTG 615
           ++G R L+   G++  +++RV +AG FG  I  + A+ +GM+PD P ++    GN +  G
Sbjct: 507 FAGLRTLLSLVGLEAASLERVYIAGGFGRFIDVEDAIGIGMLPDLPRERYAYVGNTSLKG 566

Query: 616 ARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPN-SAEPFP 665
           AR+ LL+  A  E     ++I  +E +V   F E F+ A  +P+ +A+ FP
Sbjct: 567 ARLCLLSRRAWQETAELARRITYVELSVGNLFMEEFMAALFLPHTNADLFP 617


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: 932
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: 622
Length adjustment: 38
Effective length of query: 660
Effective length of database: 584
Effective search space:   385440
Effective search space used:   385440
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_015738377.1 ADEG_RS01690 (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.17956.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-110  353.6   0.0     5e-109  349.4   0.0    2.3  2  lcl|NCBI__GCF_000024605.1:WP_015738377.1  ADEG_RS01690 DUF4445 domain-cont


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738377.1  ADEG_RS01690 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.4   0.0    0.0074    0.0074     147     173 ..     261     287 ..     251     292 .. 0.84
   2 !  349.4   0.0    5e-109    5e-109       1     261 []     360     620 ..     360     620 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.0074
                                RACo_C_ter 147 iyagvktLleevglevedidkvylaGa 173
                                               ++  +  L++e+g++++di+ v+ aG 
  lcl|NCBI__GCF_000024605.1:WP_015738377.1 261 VNGLIDELCREAGISFKDIRAVVGAGN 287
                                               5566788****************9997 PP

  == domain 2  score: 349.4 bits;  conditional E-value: 5e-109
                                RACo_C_ter   1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvigne 69 
                                               e++l++DiGTN+E+vlgn++wl+a++++aGPA+EG++i+cGmrA  gAie+ve++p   ev +++++++
  lcl|NCBI__GCF_000024605.1:WP_015738377.1 360 ELTLFLDIGTNGEMVLGNREWLMACACSAGPAFEGSGITCGMRAVAGAIEEVEVSPGGEEVFYRTVDGK 428
                                               689****************************************************************** PP

                                RACo_C_ter  70 kpkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitekDid 138
                                               kp GicGsG+i+l+++ll+ag+id++g++ + l+++r+re ee +e+vlv+ e++++++di++t+ D++
  lcl|NCBI__GCF_000024605.1:WP_015738377.1 429 KPLGICGSGLISLLSSLLRAGVIDRSGRFVEGLDTPRLREGEEGKEFVLVWGESTGHGRDIYVTQGDLQ 497
                                               ********************************************************************* PP

                                RACo_C_ter 139 elirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslag 207
                                               +l+rakaAi+ag++tLl+ vgle+ ++++vy+aG+fG++id+e+Ai iG+lPdl++e++ +vGNtsl+g
  lcl|NCBI__GCF_000024605.1:WP_015738377.1 498 NLLRAKAAIFAGLRTLLSLVGLEAASLERVYIAGGFGRFIDVEDAIGIGMLPDLPRERYAYVGNTSLKG 566
                                               ********************************************************************* PP

                                RACo_C_ter 208 AraallsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsvk 261
                                               Ar +llsr+a++e+ e+ar+ity+el+v + Fmeef+aalflpht+++lfpsvk
  lcl|NCBI__GCF_000024605.1:WP_015738377.1 567 ARLCLLSRRAWQETAELARRITYVELSVGNLFMEEFMAALFLPHTNADLFPSVK 620
                                               ***************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (622 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: 21.19
//
[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