Alignments for a candidate for ramA in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Nitriliruptor alkaliphilus DSM 45188

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_052665962.1 NITAL_RS09140 DUF4445 domain-containing protein

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



>NCBI__GCF_000969705.1:WP_052665962.1
          Length = 689

 Score =  651 bits (1679), Expect = 0.0
 Identities = 344/675 (50%), Positives = 464/675 (68%), Gaps = 19/675 (2%)

Query: 23  VVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHGVTVAD 82
           +VFTPSG  G    GT VL AAR+LGVDLDSVC GR IC +CQ+ PS G F K  +TV  
Sbjct: 15  IVFTPSGLSGTVAEGTSVLDAARELGVDLDSVCSGRAICGRCQVVPSVGTFPKWDMTVRP 74

Query: 83  DALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEARDIT 142
           D + + + +E  Y  +R + DG RLGC  ++ GD+V+DVPP SQ+H+Q+VRK     ++ 
Sbjct: 75  DHVVDPDDLEGHYVGRRPIADGHRLGCALRIVGDLVVDVPPASQIHKQIVRKDIGLGELR 134

Query: 143 MNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPALRKGGWK 202
           ++P   L YV  ++ D       ++R+  AL   WDL  V+ D  +L  L  A+      
Sbjct: 135 IDPVVTLRYVAFDDDDAGAGASVLDRIRAALARTWDLHDVQVDAEVLPHLHRAVADPTDG 194

Query: 203 VTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVASSGIMN 262
            T+AV     +H  +I   WPG+ + S+ G+A+D+GSTT+A +LCDL +G+V+A++G MN
Sbjct: 195 ATLAVR----DH--RIAAAWPGYVDRSV-GVAIDIGSTTVAGYLCDLSSGEVLATAGRMN 247

Query: 263 PQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVFVCN 322
           PQIRFGEDLMSRVSY M+N GGD+ +T AVR+ ++ L T++AA+A ++++ +++ V V N
Sbjct: 248 PQIRFGEDLMSRVSYVMLNPGGDRTLTAAVRQALSELVTELAADAAVERSQVLELVLVGN 307

Query: 323 PVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGADAA 382
           P+MHHL LGIDP  LGQ+PF LAT   + LRA +LD+   P  RVYL PCIAGHVGAD A
Sbjct: 308 PIMHHLVLGIDPTPLGQSPFTLATGEPVELRAADLDIPA-PFGRVYLAPCIAGHVGADTA 366

Query: 383 AVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAAPGA 442
           A  L+E P + + + L++DVGTNAEI++G++  + A SSPTGPAFEGAQIS GQRA  GA
Sbjct: 367 AAILAEGPHRGDAVQLLIDVGTNAEIVVGDRRALYAASSPTGPAFEGAQISCGQRATTGA 426

Query: 443 IERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATT-GITGICGSGIIEAIAEMRMAGLL 501
           +ERV I+  T EPRFRVIG D WSDE+GF AAVA + G+TG+CGSGIIE I E+ +AG++
Sbjct: 427 VERVRIDRTTLEPRFRVIGCDRWSDEEGFTAAVADSGGVTGVCGSGIIEVIGELFLAGII 486

Query: 502 DASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEG-GPTITVTNPDIRAIQMAKAALYSG 560
           D  G+I +     T R + DGRT++Y+L+D   EG G  + +T  D+RAIQ+AKAAL +G
Sbjct: 487 DQRGVIRAELAERTDRVVADGRTHSYVLYD---EGPGAQLRITQDDVRAIQLAKAALRAG 543

Query: 561 ARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIAL 620
             LL++  G+D +D V LAGAFGAHI  ++A+VLG++PD PLD V S GNAAG+GA  AL
Sbjct: 544 TDLLLEHAGLDRIDEVRLAGAFGAHIDPRYALVLGLVPDVPLDAVRSVGNAAGSGAVRAL 603

Query: 621 LNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIVTLPEANFNT 680
           L+ + R E+EATV+ I KIETA EPRFQE FV A A P++  P   L+ +V LP +    
Sbjct: 604 LSGDKRREMEATVRTITKIETATEPRFQELFVAALAFPHATAPSTHLAEVVDLPASR--- 660

Query: 681 GGGDGNEVGGRRRRR 695
                +   GRRRRR
Sbjct: 661 ---PASPPTGRRRRR 672


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: 1235
Number of extensions: 51
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: 689
Length adjustment: 39
Effective length of query: 659
Effective length of database: 650
Effective search space:   428350
Effective search space used:   428350
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_052665962.1 NITAL_RS09140 (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.8228.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-89  285.5   0.0    2.4e-89  284.9   0.0    1.2  1  lcl|NCBI__GCF_000969705.1:WP_052665962.1  NITAL_RS09140 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052665962.1  NITAL_RS09140 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.9   0.0   2.4e-89   2.4e-89       2     254 ..     380     645 ..     379     650 .. 0.97

  Alignments for each domain:
  == domain 1  score: 284.9 bits;  conditional E-value: 2.4e-89
                                RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek 70 
                                               ++lliD+GTNaEiv+g++  l+aas+++GPA+EG++i+cG+rA++gA+erv+id++tle++++vig+++
  lcl|NCBI__GCF_000969705.1:WP_052665962.1 380 VQLLIDVGTNAEIVVGDRRALYAASSPTGPAFEGAQISCGQRATTGAVERVRIDRTTLEPRFRVIGCDR 448
                                               689****************************************************************99 PP

                                RACo_C_ter  71 ................pkGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvla 121
                                                               ++G+cGsGii++i el++agiid++g ++ el  +++r+ ++ +t++yvl+++
  lcl|NCBI__GCF_000969705.1:WP_052665962.1 449 wsdeegftaavadsggVTGVCGSGIIEVIGELFLAGIIDQRGVIRAELaeRTDRVVADGRTHSYVLYDE 517
                                               99******************************************999877899*************987 PP

                                RACo_C_ter 122 eesetekdivitekDidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllP 190
                                                    ++++ it+ D+++++ akaA++ag+ +Lle++g  +++id+v laGafG++id+++A+++Gl+P
  lcl|NCBI__GCF_000969705.1:WP_052665962.1 518 G---PGAQLRITQDDVRAIQLAKAALRAGTDLLLEHAG--LDRIDEVRLAGAFGAHIDPRYALVLGLVP 581
                                               5...5679******************************..99*************************** PP

                                RACo_C_ter 191 dlelekvkqvGNtslagAraallsreareeleeiarkityielavekkFmeefvaalflphtdl 254
                                               d++l+ v++vGN++++gA  alls ++r+e+e+ +r+it+ie+a+e++F+e fvaal++ph ++
  lcl|NCBI__GCF_000969705.1:WP_052665962.1 582 DVPLDAVRSVGNAAGSGAVRALLSGDKRREMEATVRTITKIETATEPRFQELFVAALAFPHATA 645
                                               *************************************************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (689 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: 23.01
//
[ok]

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

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

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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