Alignments for a candidate for ramA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfovibrio vulgaris Miyazaki F

Align ATP-dependent reduction of co(II)balamin (RamA-like) (characterized)
to candidate 8500650 DvMF_1398 iron-sulfur cluster-binding protein, putative (RefSeq)

Query= reanno::Miya:8500650
         (685 letters)



>FitnessBrowser__Miya:8500650
          Length = 685

 Score = 1365 bits (3532), Expect = 0.0
 Identities = 685/685 (100%), Positives = 685/685 (100%)

Query: 1   MSPHSSSEQPPCPAGNDTGCATARPEGRSGPVTPATPDRPGCPSTPGTQPASGAAAEVTL 60
           MSPHSSSEQPPCPAGNDTGCATARPEGRSGPVTPATPDRPGCPSTPGTQPASGAAAEVTL
Sbjct: 1   MSPHSSSEQPPCPAGNDTGCATARPEGRSGPVTPATPDRPGCPSTPGTQPASGAAAEVTL 60

Query: 61  PDGRILHLPLSQSVSLSGQAAAGAAPASTLAQLVWMSGQVDPPALCSGLGRCGRCAARFT 120
           PDGRILHLPLSQSVSLSGQAAAGAAPASTLAQLVWMSGQVDPPALCSGLGRCGRCAARFT
Sbjct: 61  PDGRILHLPLSQSVSLSGQAAAGAAPASTLAQLVWMSGQVDPPALCSGLGRCGRCAARFT 120

Query: 121 RGTPAPHPAEEAHFSPAELADGWRLLCRHALPAPASRSPSSPQGTDPNGNAASPPDARCT 180
           RGTPAPHPAEEAHFSPAELADGWRLLCRHALPAPASRSPSSPQGTDPNGNAASPPDARCT
Sbjct: 121 RGTPAPHPAEEAHFSPAELADGWRLLCRHALPAPASRSPSSPQGTDPNGNAASPPDARCT 180

Query: 181 MAFTLPAGSAPRRFRAADAPLPDAIQASATGTSPATYTSPATGTSPATGTSPATGAPLLL 240
           MAFTLPAGSAPRRFRAADAPLPDAIQASATGTSPATYTSPATGTSPATGTSPATGAPLLL
Sbjct: 181 MAFTLPAGSAPRRFRAADAPLPDAIQASATGTSPATYTSPATGTSPATGTSPATGAPLLL 240

Query: 241 AIDLGTTTLHWSALTPDGRRVAHGAELNPQMGAGSEVMSRLAVASSPQGLAALRRLTLAA 300
           AIDLGTTTLHWSALTPDGRRVAHGAELNPQMGAGSEVMSRLAVASSPQGLAALRRLTLAA
Sbjct: 241 AIDLGTTTLHWSALTPDGRRVAHGAELNPQMGAGSEVMSRLAVASSPQGLAALRRLTLAA 300

Query: 301 VARIAAGLPGPVRGLCVAGNSAMTAILLGHDVSGLATAPYRLDYAGGTAEILPELADVTY 360
           VARIAAGLPGPVRGLCVAGNSAMTAILLGHDVSGLATAPYRLDYAGGTAEILPELADVTY
Sbjct: 301 VARIAAGLPGPVRGLCVAGNSAMTAILLGHDVSGLATAPYRLDYAGGTAEILPELADVTY 360

Query: 361 RAGLPDLPDSPGRAAVPEVWIPPQPAPFVGGDVGAGMAALLYGGLVSGGGAGVAANTLQA 420
           RAGLPDLPDSPGRAAVPEVWIPPQPAPFVGGDVGAGMAALLYGGLVSGGGAGVAANTLQA
Sbjct: 361 RAGLPDLPDSPGRAAVPEVWIPPQPAPFVGGDVGAGMAALLYGGLVSGGGAGVAANTLQA 420

Query: 421 AATAPAPAASPRFPFLLADLGTNGEFVLATGPDSALVTSVALGPALEGIGLSCGGVAQPG 480
           AATAPAPAASPRFPFLLADLGTNGEFVLATGPDSALVTSVALGPALEGIGLSCGGVAQPG
Sbjct: 421 AATAPAPAASPRFPFLLADLGTNGEFVLATGPDSALVTSVALGPALEGIGLSCGGVAQPG 480

Query: 481 AIAAFTLGPAGLAPTVLPEDDGAPAAPTHLCGTGYLSLLRVLLRAGLLDEDGRFVMEPHS 540
           AIAAFTLGPAGLAPTVLPEDDGAPAAPTHLCGTGYLSLLRVLLRAGLLDEDGRFVMEPHS
Sbjct: 481 AIAAFTLGPAGLAPTVLPEDDGAPAAPTHLCGTGYLSLLRVLLRAGLLDEDGRFVMEPHS 540

Query: 541 PLARRLAASLVEVRGERRLPLPGGLHLSAGDVEEVLKVKAAFSLAYERLLAEAGMSGTAL 600
           PLARRLAASLVEVRGERRLPLPGGLHLSAGDVEEVLKVKAAFSLAYERLLAEAGMSGTAL
Sbjct: 541 PLARRLAASLVEVRGERRLPLPGGLHLSAGDVEEVLKVKAAFSLAYERLLAEAGMSGTAL 600

Query: 601 DAVYLAGALGEHARPDDLETLGFLPAGVAGRTRAVGNASLRGAELLLLQPELRARINAWR 660
           DAVYLAGALGEHARPDDLETLGFLPAGVAGRTRAVGNASLRGAELLLLQPELRARINAWR
Sbjct: 601 DAVYLAGALGEHARPDDLETLGFLPAGVAGRTRAVGNASLRGAELLLLQPELRARINAWR 660

Query: 661 TGCRVVDLTTASDFSAAFLRHMRFR 685
           TGCRVVDLTTASDFSAAFLRHMRFR
Sbjct: 661 TGCRVVDLTTASDFSAAFLRHMRFR 685


Lambda     K      H
   0.316    0.133    0.403 

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: 2461
Number of extensions: 177
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: 685
Length of database: 685
Length adjustment: 39
Effective length of query: 646
Effective length of database: 646
Effective search space:   417316
Effective search space used:   417316
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 (21.6 bits)
S2: 54 (25.4 bits)

Align candidate 8500650 DvMF_1398 (iron-sulfur cluster-binding protein, putative (RefSeq))
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.11706.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.9e-46  143.7   0.0    4.1e-46  143.2   0.0    1.2  1  lcl|FitnessBrowser__Miya:8500650  DvMF_1398 iron-sulfur cluster-bi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500650  DvMF_1398 iron-sulfur cluster-binding protein, putative (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   4.1e-46   4.1e-46       4     248 ..     436     683 ..     434     685 .] 0.91

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 4.1e-46
                        RACo_C_ter   4 lliDiGTNaEivlgnk.dwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek...pkGicG 76 
                                       ll D+GTN+E vl +  d  l++s a GPAlEG +++cG  A+pgAi  +++ p+ l +++   ++ +   p+ +cG
  lcl|FitnessBrowser__Miya:8500650 436 LLADLGTNGEFVLATGpDSALVTSVALGPALEGIGLSCGGVAQPGAIAAFTLGPAGLAPTVLPEDDGApaaPTHLCG 512
                                       899**********8754999************************************99999988764445599**** PP

                        RACo_C_ter  77 sGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitekDidelirakaAiyagvkt 153
                                       +G ++l+  ll+ag++d++g++  e +s+  r+      + +  +++      + ++  D++e+++ kaA   +++ 
  lcl|FitnessBrowser__Miya:8500650 513 TGYLSLLRVLLRAGLLDEDGRFVMEPHSPLARRLAAS-LVEVRGERRLPLPGGLHLSAGDVEEVLKVKAAFSLAYER 588
                                       **********************999777777654432.33333444455678************************* PP

                        RACo_C_ter 154 LleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAraallsreareeleeiarkity 230
                                       Ll e+g++ + +d vylaGa G++  +++  t+G lP   + ++++vGN+sl+gA+ +ll++e r+++++ ++  + 
  lcl|FitnessBrowser__Miya:8500650 589 LLAEAGMSGTALDAVYLAGALGEHARPDDLETLGFLPAGVAGRTRAVGNASLRGAELLLLQPELRARINAWRTGCRV 665
                                       ***************************************************************************** PP

                        RACo_C_ter 231 ielavekkFmeefvaalf 248
                                       ++l ++++F   f++ + 
  lcl|FitnessBrowser__Miya:8500650 666 VDLTTASDFSAAFLRHMR 683
                                       *************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (685 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: 14.46
//
[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