Alignments for a candidate for ramA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfovibrio vulgaris Hildenborough

Align ATP-dependent reduction of co(II)balamin (characterized)
to candidate 206336 DVU0908 iron-sulfur cluster-binding protein, putative

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



>MicrobesOnline__882:206336
          Length = 543

 Score = 1086 bits (2808), Expect = 0.0
 Identities = 543/543 (100%), Positives = 543/543 (100%)

Query: 1   MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV 60
           MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV
Sbjct: 1   MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV 60

Query: 61  RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP 120
           RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP
Sbjct: 61  RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP 120

Query: 121 FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV 180
           FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV
Sbjct: 121 FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV 180

Query: 181 LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV 240
           LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV
Sbjct: 181 LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV 240

Query: 241 EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA 300
           EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA
Sbjct: 241 EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA 300

Query: 301 DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD 360
           DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD
Sbjct: 301 DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD 360

Query: 361 GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR 420
           GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR
Sbjct: 361 GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR 420

Query: 421 GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF 480
           GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF
Sbjct: 421 GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF 480

Query: 481 IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH 540
           IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH
Sbjct: 481 IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH 540

Query: 541 FHF 543
           FHF
Sbjct: 541 FHF 543


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: 1273
Number of extensions: 46
Number of successful extensions: 1
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: 543
Length adjustment: 35
Effective length of query: 508
Effective length of database: 508
Effective search space:   258064
Effective search space used:   258064
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: 52 (24.6 bits)

Align candidate 206336 DVU0908 (iron-sulfur cluster-binding protein, putative)
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.8632.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    7.2e-45  139.1   0.0    1.2e-44  138.5   0.0    1.2  1  lcl|MicrobesOnline__882:206336  DVU0908 iron-sulfur cluster-bind


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206336  DVU0908 iron-sulfur cluster-binding protein, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.0   1.2e-44   1.2e-44       4     249 ..     298     541 ..     296     542 .. 0.89

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 1.2e-44
                      RACo_C_ter   4 lliDiGTNaEivlg.nkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignekpkGicGsGiid 81 
                                     +l D+GTN+E vl  + ++ l++s a GPAlEG ++++G+ A++gAi +++++p  l +   v+++ ++ Gi G+G i+
  lcl|MicrobesOnline__882:206336 298 VLADLGTNGEFVLAlSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVP--YVLDGGEADGISGTGYIS 374
                                     678**********736799*************************************555..5678888*********** PP

                      RACo_C_ter  82 liaelleagiidkkgklnkelkserireeeeteeyvlvlaeeset..ekdivitekDidelirakaAiyagvktLleev 158
                                     l+ +ll+ag++d +g++ ++ +s+      ++ + ++ ++ e      + +++  +Di+e+++ kaA   +++ Ll ++
  lcl|MicrobesOnline__882:206336 375 LVHALLRAGLLDVDGRFIQSPSSPLAA---RMARSIVSHRGEPCLplARGLYLAARDIEEILKVKAAFSLAFERLLATA 450
                                     *****************7775444433...3444444333333322378****************************** PP

                      RACo_C_ter 159 glevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAraallsreareeleeiarkityielavek 237
                                     ++  + ++ + laGa G++  +++   +G +P  +  ++++vGNtsl+gA+ +l+s+  r++l++ ++  t ++l +++
  lcl|MicrobesOnline__882:206336 451 QMPSHALSGIHLAGALGQHALPADLEGLGFIPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAP 529
                                     ******************************************************************************* PP

                      RACo_C_ter 238 kFmeefvaalfl 249
                                     +F   f++ + +
  lcl|MicrobesOnline__882:206336 530 DFSAAFLRHMHF 541
                                     ******998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (543 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: 00:00:00.00
# Mc/sec: 16.50
//
[ok]

This GapMind analysis is from Apr 09 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