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_051327315.1 G491_RS0116500 DUF4445 domain-containing protein

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



>NCBI__GCF_000429905.1:WP_051327315.1
          Length = 524

 Score =  239 bits (611), Expect = 2e-67
 Identities = 164/529 (31%), Positives = 264/529 (49%), Gaps = 31/529 (5%)

Query: 152 VEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPALRKGGWKVTVAVHLGD 211
           VE+  P +   T  +ERL   L+       +  D+ +L  L   LR G   +     L  
Sbjct: 22  VEIPAPSLENNTAFVERLCSQLEKPMGGMKISVDMEVLKALPKILRTGEGAMDCT--LFG 79

Query: 212 ENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVASSGIMNPQIRFGEDL 271
           +     ++ + P    G + GLAVDLG+T +   L D++TG V+  S   NPQ R G D+
Sbjct: 80  QGGEAVLVGVAPK-KAGPLPGLAVDLGTTRVVLRLVDMRTGQVLKESSFDNPQGRIGPDV 138

Query: 272 MSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVFVCNPVMHHLFLG 331
           ++R+ Y+   +GG +E+   + +G++    ++AA   +    +       N  M HL LG
Sbjct: 139 LARIHYAEQ-EGGLEELQSHIGQGISQEGARLAAACGLSPKDVYCVAAAGNTAMTHLLLG 197

Query: 332 IDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGADAAAVALSEAPD 391
            DP+ + + P+    ++   L+  ++ L+   +ARVY+ P +  + G D  A  LS    
Sbjct: 198 ADPYWIIREPYTPMVNSPGFLKCRDIGLDFAKSARVYVFPNVGSYFGGDLLAGILSSDMY 257

Query: 392 KSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAAPGAIERVEINPE 451
             ED+ ++VDVGTNAE+++GNKD ++AC+   GPA EG   + G  A PGAIE+V I+P+
Sbjct: 258 CKEDVSMLVDVGTNAEVVVGNKDWLMACAGAAGPALEGGVTAMGMLAGPGAIEKVRIDPK 317

Query: 452 TKEPRFRVIGSDIWSDEDGFAAAVATTGI--TGICGSGIIEAIAEMRMAGLLDASG-LIG 508
           T+E  F+ IG                 GI   GICGSG+I+  A++ +AG++D  G L+ 
Sbjct: 318 TREFVFQTIG-----------------GIKPVGICGSGVIDLAAQLFLAGMIDLRGKLVP 360

Query: 509 SAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKAALYSGARLLMDKF 568
           SA +   T   QD      ++       G  +  +  D+ ++  +KAA+Y+  R + +  
Sbjct: 361 SACEGRLTE--QDEIPALIIVSKEDSANGRALLFSQADLDSLVRSKAAMYTILRTITNTV 418

Query: 569 GIDTVD--RVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIALLNTEAR 626
           G+   D     +AG FG++I    A+ +GMIPD PL    + GN +  GA   LL  EA 
Sbjct: 419 GLAFTDLAEFNIAGTFGSYIDPVSAITIGMIPDLPLSTYKALGNTSLEGATQVLLQREAV 478

Query: 627 SEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIVTLPE 675
             +    ++I  +E  V   F   F  A  IP++    P L   V +P+
Sbjct: 479 GVVREIREKITYMELNVNQEFMNRFSAAKFIPHTN---PALFPSVKIPQ 524


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: 781
Number of extensions: 30
Number of successful extensions: 4
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: 524
Length adjustment: 37
Effective length of query: 661
Effective length of database: 487
Effective search space:   321907
Effective search space used:   321907
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_051327315.1 G491_RS0116500 (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.15027.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-103  330.5   0.4   1.2e-102  328.5   0.1    1.9  2  lcl|NCBI__GCF_000429905.1:WP_051327315.1  G491_RS0116500 DUF4445 domain-co


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_051327315.1  G491_RS0116500 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.025     0.025     182     206 ..     169     192 ..     158     196 .. 0.85
   2 !  328.5   0.1  1.2e-102  1.2e-102       2     261 .]     262     521 ..     261     521 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.025
                                RACo_C_ter 182 kAitiGllPdlelekvkqvGNtsla 206
                                                A   Gl P+ ++  v ++GNt+++
  lcl|NCBI__GCF_000429905.1:WP_051327315.1 169 LAAACGLSPK-DVYCVAAAGNTAMT 192
                                               578899***9.999*******9986 PP

  == domain 2  score: 328.5 bits;  conditional E-value: 1.2e-102
                                RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek 70 
                                               +s+l+D+GTNaE+v+gnkdwl+a+++aaGPAlEGg + +Gm A pgAie+v+idp+t e+ +++ig+ k
  lcl|NCBI__GCF_000429905.1:WP_051327315.1 262 VSMLVDVGTNAEVVVGNKDWLMACAGAAGPALEGGVTAMGMLAGPGAIEKVRIDPKTREFVFQTIGGIK 330
                                               79******************************************************************* PP

                                RACo_C_ter  71 pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitekDide 139
                                               p+GicGsG+idl a+l++ag+id +gkl  ++++ r++e++e++++++v++e+s++++ ++++++D+d+
  lcl|NCBI__GCF_000429905.1:WP_051327315.1 331 PVGICGSGVIDLAAQLFLAGMIDLRGKLVPSACEGRLTEQDEIPALIIVSKEDSANGRALLFSQADLDS 399
                                               ********************************************************************* PP

                                RACo_C_ter 140 lirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagA 208
                                               l+r+kaA+y++++t++++vgl+++d+ ++ +aG+fGsyid+ +AitiG++Pdl+l+++k++GNtsl+gA
  lcl|NCBI__GCF_000429905.1:WP_051327315.1 400 LVRSKAAMYTILRTITNTVGLAFTDLAEFNIAGTFGSYIDPVSAITIGMIPDLPLSTYKALGNTSLEGA 468
                                               ********************************************************************* PP

                                RACo_C_ter 209 raallsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsvk 261
                                               +++ll+rea+  ++ei++kity+el+v+++Fm++f+aa f+pht+  lfpsvk
  lcl|NCBI__GCF_000429905.1:WP_051327315.1 469 TQVLLQREAVGVVREIREKITYMELNVNQEFMNRFSAAKFIPHTNPALFPSVK 521
                                               **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (524 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: 14.14
//
[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