Alignments for a candidate for ramA in Desulfacinum infernum DSM 9756

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfacinum infernum DSM 9756

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_084076482.1 BUB04_RS13150 DUF4445 domain-containing protein

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



>NCBI__GCF_900129305.1:WP_084076482.1
          Length = 718

 Score =  305 bits (780), Expect = 7e-87
 Identities = 203/667 (30%), Positives = 328/667 (49%), Gaps = 57/667 (8%)

Query: 15  TDPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGE-- 72
           T  A+   V F P  +      G  +L  A   G+ ++S+CGG+G+C KC++    GE  
Sbjct: 65  TQMANRIKVTFQPENRVVEAGPGETLLDVAALAGIYINSLCGGQGVCGKCRLKVLSGEVE 124

Query: 73  FSKHGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQG-DVVIDVPPESQVHRQV 131
           FS  G+                + D++ + +G  L CQ+ ++  DV + +PPES+   + 
Sbjct: 125 FSSRGIG---------------FLDRKEVDEGYVLACQSTLKDRDVEVWIPPESRREEEQ 169

Query: 132 V-------------RKRAEARDITM---NPSTRLYYVEVEEPDMHKPTGDMERLIEALDA 175
           +              + A A  + +    P     ++++ EP +     D+ER+  AL  
Sbjct: 170 ILMVDNIVQYGAPSSQEAGAAPVPVPYYEPLCHKVFLKLPEPTLKDNLSDLERIYRALAQ 229

Query: 176 QWDLKGVKTDLHILSVLQPALRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAV 235
           ++     + D   L  L   LR   W+VT  VH  D +H   +  + PG    + YG+AV
Sbjct: 230 KFPDVKWEADFACLRNLARLLRDNHWEVTALVHALD-SHCHHVRSLEPGDTTRNAYGVAV 288

Query: 236 DLGSTTIAAHLCDLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREG 295
           D+G+TTI A L DLK+  VV      N Q R+GED++SR+ Y+    GG   +  AV   
Sbjct: 289 DVGTTTIVAQLVDLKSSQVVGVEASHNQQARYGEDVISRMIYAC-GHGGLDPLKNAVVTT 347

Query: 296 MNALFTQIAAEAEIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAV 355
           +N L   + A A I    I+  V   N  M HL LG++P  +   P+    +     RA 
Sbjct: 348 INTLVNSLVAGAGIQHTDIISFVAAGNTTMTHLLLGLEPCTIRLEPYIPTATRIPWARAA 407

Query: 356 ELDLNIHPAARVYLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDK 415
           E+ L  HP A ++ +PC++ +VG D  A  L+   + S  L  ++D+GTN EI++GN + 
Sbjct: 408 EVGLTGHPDALLHCMPCVSSYVGGDITAGVLACGMNDSPQLSALIDIGTNGEIVVGNNEW 467

Query: 416 VLACSSPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAV 475
           ++ CS+  GPAFEG     G RA  GA+++V I  +  E   + IG              
Sbjct: 468 LVCCSASAGPAFEGGGTKCGMRATKGAVQKVRIRGDRLE--IQTIGGG------------ 513

Query: 476 ATTGITGICGSGIIEAIAEMRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVE 535
                 GICGSG+I+ +AE+   G++D SG     +         DG     L  +   E
Sbjct: 514 ---KARGICGSGLIDCMAELVAEGIIDQSGKFVRLDHPRVREV--DGVPEFVLAKETESE 568

Query: 536 GGPTITVTNPDIRAIQMAKAALYSGARLLMDKFGI--DTVDRVVLAGAFGAHISAKHAMV 593
            G  + +T  DI  +  +KAA+ +  ++L++  G+    +DR+ +AG FGAH+  + ++ 
Sbjct: 569 TGEPVVITEDDIGNLMKSKAAVLAAMKVLLESLGLRFSDLDRLYVAGGFGAHLDIEKSIR 628

Query: 594 LGMIPDCPLDKVTSAGNAAGTGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVN 653
           +G++PD P +KV   GN++  GAR ALL+T A  +  A  +Q+   E +V P F + FV 
Sbjct: 629 IGLLPDVPREKVLFIGNSSLGGARQALLSTHAYRKANAIARQMTYFELSVHPGFMDEFVA 688

Query: 654 ASAIPNS 660
           A  +P++
Sbjct: 689 ALFLPHT 695


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: 1015
Number of extensions: 50
Number of successful extensions: 5
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: 718
Length adjustment: 39
Effective length of query: 659
Effective length of database: 679
Effective search space:   447461
Effective search space used:   447461
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: 55 (25.8 bits)

Align candidate WP_084076482.1 BUB04_RS13150 (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.28435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-107  344.1   0.1   1.5e-106  341.3   0.0    2.0  2  lcl|NCBI__GCF_900129305.1:WP_084076482.1  BUB04_RS13150 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_084076482.1  BUB04_RS13150 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.017     0.017     146     173 ..     347     374 ..     339     380 .. 0.77
   2 !  341.3   0.0  1.5e-106  1.5e-106       2     261 .]     448     704 ..     447     704 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.017
                                RACo_C_ter 146 AiyagvktLleevglevedidkvylaGa 173
                                                i++ v+ L+  +g++ +di +++ aG 
  lcl|NCBI__GCF_900129305.1:WP_084076482.1 347 TINTLVNSLVAGAGIQHTDIISFVAAGN 374
                                               4566666677779*************97 PP

  == domain 2  score: 341.3 bits;  conditional E-value: 1.5e-106
                                RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek 70 
                                               +s liDiGTN+Eiv+gn++wl+++sa+aGPA+EGg++kcGmrA++gA+++v+i+ +   +e+++ig+ k
  lcl|NCBI__GCF_900129305.1:WP_084076482.1 448 LSALIDIGTNGEIVVGNNEWLVCCSASAGPAFEGGGTKCGMRATKGAVQKVRIRGDR--LEIQTIGGGK 514
                                               6789**************************************************999..999******* PP

                                RACo_C_ter  71 pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitekDide 139
                                               ++GicGsG+id++ael+ +giid++gk+ + l+++r+re ++ +e+vl++++eset++ +vite Di +
  lcl|NCBI__GCF_900129305.1:WP_084076482.1 515 ARGICGSGLIDCMAELVAEGIIDQSGKFVR-LDHPRVREVDGVPEFVLAKETESETGEPVVITEDDIGN 582
                                               ****************************66.79************************************ PP

                                RACo_C_ter 140 lirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagA 208
                                               l+++kaA+ a++k+Lle++gl+++d+d++y+aG+fG+++d+ek+i+iGllPd+++ekv ++GN+sl gA
  lcl|NCBI__GCF_900129305.1:WP_084076482.1 583 LMKSKAAVLAAMKVLLESLGLRFSDLDRLYVAGGFGAHLDIEKSIRIGLLPDVPREKVLFIGNSSLGGA 651
                                               ********************************************************************* PP

                                RACo_C_ter 209 raallsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsvk 261
                                               r+alls++a++++++iar++ty+el+v++ Fm+efvaalflphtd +lfpsv+
  lcl|NCBI__GCF_900129305.1:WP_084076482.1 652 RQALLSTHAYRKANAIARQMTYFELSVHPGFMDEFVAALFLPHTDQSLFPSVQ 704
                                               **************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (718 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: 15.04
//
[ok]

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

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Protein sequences (fasta format)
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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