Alignments for a candidate for ramA in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Malonomonas rubra DSM 5091

Align ATP-dependent reduction of co(II)balamin (characterized)
to candidate WP_072906133.1 BUB13_RS04880 DUF4445 domain-containing protein

Query= reanno::DvH:206336
         (543 letters)



>NCBI__GCF_900142125.1:WP_072906133.1
          Length = 409

 Score =  149 bits (376), Expect = 2e-40
 Identities = 136/432 (31%), Positives = 198/432 (45%), Gaps = 42/432 (9%)

Query: 123 LAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELVLQ 182
           L +DLGTTSL   +   +G V A+ S  NPQ   G+DV++R+  A       +L+ L++ 
Sbjct: 6   LGLDLGTTSLIGRIWTTEGQVVAEASCDNPQQQFGADVIARMEAALKGAA-DQLQALLVD 64

Query: 183 ALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESVEG 242
            + R++AD+               G EP         +     A N A++ +L  ESVE 
Sbjct: 65  GINRLIADLLKQV-----------GAEP-------GWISAAAAAANPAISLLLVRESVEN 106

Query: 243 LASAPYRLEMRGGTALALPGL-----PPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPF 297
           +   PYR + R G AL    L      P  + PL + +VGGDL A    +L D     P 
Sbjct: 107 VLQPPYRPDYRAGEALGSGKLGIDLPAPLLLLPLVSGYVGGDLLA---LLLADPPKDGPT 163

Query: 298 VLADLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPY 357
           +  DLGTN E  L    +  LVTSVA GPA E   L  G     GA+T   +     V  
Sbjct: 164 LYLDLGTNAELAL-WDGDSWLVTSVAAGPAFEAGNLGCGMRHGFGAVTEVGVLRDRFVYT 222

Query: 358 VLDGGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLP 417
           V  GG   GI G+G  SL+   +++GL+ +DGR     +S + + ++R +V+    P L 
Sbjct: 223 VAGGGTPKGICGSGLFSLLSRAIQSGLIAIDGRI--KEASEVDSNLSRYLVADENGPALQ 280

Query: 418 LARG----LYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPA 473
           L R     L L   D+      K A       LL    + +  L+ + LAGALG  ALPA
Sbjct: 281 LYRDARTCLRLTQDDVRAFQLAKGAVLAGVNCLLERKGIQAEQLASVRLAGALG-GALPA 339

Query: 474 D-LEGLGFIPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVV---DLTAAP 529
           + L+G+  +P     + R +    L G + +L     +D L   R+  T +    L+  P
Sbjct: 340 EALKGVALLPENVIDKCRFLPGAVLIGLQRVLQR---KDGLEQARQLATELKPYPLSGTP 396

Query: 530 DFSAAFLRHMHF 541
            F  AFL  + F
Sbjct: 397 AFEKAFLGSLDF 408


Lambda     K      H
   0.320    0.136    0.413 

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: 544
Number of extensions: 34
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: 543
Length of database: 409
Length adjustment: 33
Effective length of query: 510
Effective length of database: 376
Effective search space:   191760
Effective search space used:   191760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_072906133.1 BUB13_RS04880 (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.7371.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.4e-51  159.9   0.1    8.3e-51  158.6   0.0    1.6  2  lcl|NCBI__GCF_900142125.1:WP_072906133.1  BUB13_RS04880 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072906133.1  BUB13_RS04880 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   1.5      0.18      0.18      20      33 ..      82      95 ..      79      96 .. 0.88
   2 !  158.6   0.0   8.3e-51   8.3e-51       3     247 ..     163     406 ..     161     409 .] 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.18
                                RACo_C_ter 20 dwllaasaaaGPAl 33
                                               w+ aa+aaa PA+
  lcl|NCBI__GCF_900142125.1:WP_072906133.1 82 GWISAAAAAANPAI 95
                                              6999********97 PP

  == domain 2  score: 158.6 bits;  conditional E-value: 8.3e-51
                                RACo_C_ter   3 slliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignekp 71 
                                               +l++D+GTNaE++l + d  l++s aaGPA+E g++ cGmr   gA+ +v + ++   + ++v g+ +p
  lcl|NCBI__GCF_900142125.1:WP_072906133.1 163 TLYLDLGTNAELALWDGDSWLVTSVAAGPAFEAGNLGCGMRHGFGAVTEVGVLRDR--FVYTVAGGGTP 229
                                               899*************************************************9998..99********* PP

                                RACo_C_ter  72 kGicGsGiidliaelleagiidkkgklnkel.....kserireeeeteeyvlvlaeesetekdivitek 135
                                               kGicGsG+ +l+++++++g+i  +g++++        s+ + ++e+ +++ l+ +     ++ + +t+ 
  lcl|NCBI__GCF_900142125.1:WP_072906133.1 230 KGICGSGLFSLLSRAIQSGLIAIDGRIKEASevdsnLSRYLVADENGPALQLYRDA----RTCLRLTQD 294
                                               ***************************88764433223334456677777776654....3479***** PP

                                RACo_C_ter 136 DidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNts 204
                                               D+++++ ak+A+ agv++Lle+ g+++e++ +v laGa G  + +e    + llP+  ++k +++  + 
  lcl|NCBI__GCF_900142125.1:WP_072906133.1 295 DVRAFQLAKGAVLAGVNCLLERKGIQAEQLASVRLAGALGGALPAEALKGVALLPENVIDKCRFLPGAV 363
                                               ********************************************************************* PP

                                RACo_C_ter 205 lagAraallsreareeleeiarkityielavekkFmeefvaal 247
                                               l g + +l  ++ +e+++++a++++   l+ +++F++ f+ +l
  lcl|NCBI__GCF_900142125.1:WP_072906133.1 364 LIGLQRVLQRKDGLEQARQLATELKPYPLSGTPAFEKAFLGSL 406
                                               ***************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (409 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: 00:00:00.01
# Mc/sec: 9.10
//
[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