Alignments for a candidate for ramA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Dinoroseobacter shibae DFL-12

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate 3608276 Dshi_1680 ferredoxin (RefSeq)

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



>FitnessBrowser__Dino:3608276
          Length = 690

 Score =  960 bits (2482), Expect = 0.0
 Identities = 485/684 (70%), Positives = 559/684 (81%), Gaps = 6/684 (0%)

Query: 16  DPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSK 75
           DPA+  LV+FTPSGKRGR P GT VL AAR L VDLDSVCGGRGICSKCQ+TPS+GEFSK
Sbjct: 12  DPAADALVIFTPSGKRGRVPTGTSVLDAARLLDVDLDSVCGGRGICSKCQVTPSFGEFSK 71

Query: 76  HGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKR 135
           HGV   ++AL+EWN VE RY +KRGL  GRRLGCQA + GD+VIDVP  SQVH+QVVRK 
Sbjct: 72  HGVHARENALSEWNAVEARYHEKRGLAQGRRLGCQACILGDMVIDVPATSQVHKQVVRKA 131

Query: 136 AEARDITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPA 195
           A  R +TM+P+TRL  ++V EPDMH+P+GD ERL  ALD QW +  V   L +L  LQPA
Sbjct: 132 ASQRAVTMDPATRLVLIDVAEPDMHEPSGDYERLATALDEQWQIGPVTAPLSVLRKLQPA 191

Query: 196 LRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVV 255
           LR+G W+VTVAV++ D   P +++ IWPG++EG ++GLA+DLGSTTIAAHLCDL TG V 
Sbjct: 192 LRRGKWQVTVAVNIADT--PARVIDIWPGYHEGPLWGLAIDLGSTTIAAHLCDLTTGQVA 249

Query: 256 ASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIV 315
            S+G+MNPQIRFGEDLMSRVSY+MMN  G Q MT AV + +N L T+I AEAE+    +V
Sbjct: 250 TSAGVMNPQIRFGEDLMSRVSYAMMNADGAQAMTAAVLDALNTLATEICAEAEVAPRDVV 309

Query: 316 DAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLN-IHPAARVYLLPCIA 374
           +AVFVCNPVMHHL LGIDP ELGQAPFALATS A+ L A EL L  ++PAA+ YLLPCIA
Sbjct: 310 EAVFVCNPVMHHLLLGIDPVELGQAPFALATSGAVTLSATELGLTAVNPAAQTYLLPCIA 369

Query: 375 GHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISS 434
           GHVGADAAAVALSEAPDKS++LVL+VDVGTNAEILLGN+D+VLACSSPTGPAFEGAQISS
Sbjct: 370 GHVGADAAAVALSEAPDKSDELVLIVDVGTNAEILLGNRDRVLACSSPTGPAFEGAQISS 429

Query: 435 GQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAE 494
           GQRAAPGAIERVEI+P TKEPRFRVIG ++WSD+ GFA A A TGITGICGSGIIEA+AE
Sbjct: 430 GQRAAPGAIERVEIDPVTKEPRFRVIGCELWSDDPGFAEATAATGITGICGSGIIEAVAE 489

Query: 495 MRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAK 554
           MRMAGLLDASGLIG  EQTGT R I +GRT +Y+L D    GG  I VT  DIRAIQ+AK
Sbjct: 490 MRMAGLLDASGLIGGPEQTGTPRSIAEGRTYSYVLQDDRPAGGSLIAVTQGDIRAIQLAK 549

Query: 555 AALYSGARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGT 614
           +ALY+GARLLMD+ G+DTVDRV LAGAFGAHIS KHAMVLGMIPD PLDKVTSAGNAAGT
Sbjct: 550 SALYAGARLLMDEMGVDTVDRVTLAGAFGAHISPKHAMVLGMIPDAPLDKVTSAGNAAGT 609

Query: 615 GARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIVTLP 674
           GAR+AL +  AR+EIE TV +I K+ETA+EPRFQEHFV A+AIP++  PF  L S+V LP
Sbjct: 610 GARMALCSRAARAEIEQTVSKITKVETAIEPRFQEHFVAANAIPHATAPFAHLRSVVPLP 669

Query: 675 EANFNTGGGDGNEVGGRRRRRRRG 698
           +  FN GGG      G RRRRRRG
Sbjct: 670 QPGFNAGGGG---QPGTRRRRRRG 690


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: 1357
Number of extensions: 48
Number of successful extensions: 3
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: 690
Length adjustment: 39
Effective length of query: 659
Effective length of database: 651
Effective search space:   429009
Effective search space used:   429009
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 3608276 Dshi_1680 (ferredoxin (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.8373.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    9.8e-92  292.8   0.8    1.4e-91  292.3   0.3    1.5  2  lcl|FitnessBrowser__Dino:3608276  Dshi_1680 ferredoxin (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608276  Dshi_1680 ferredoxin (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.24      0.24      35      82 ..      67     117 ..      58     138 .. 0.65
   2 !  292.3   0.3   1.4e-91   1.4e-91       1     259 [.     390     661 ..     390     663 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.24
                        RACo_C_ter  35 GgeikcGmrAapgAierveidpetlevelkvignek...pkGicGsGiidl 82 
                                       G+  k+G+ A + A+++ +  ++ ++ +    ++++      i G  +id+
  lcl|FitnessBrowser__Dino:3608276  67 GEFSKHGVHARENALSEWNAVEARYHEKRGLAQGRRlgcQACILGDMVIDV 117
                                       566789999999999888776666554444444333344455555555555 PP

  == domain 2  score: 292.3 bits;  conditional E-value: 1.4e-91
                        RACo_C_ter   1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek....... 70 
                                       e++l++D+GTNaEi lgn+d++la+s+++GPA+EG++i++G+rAapgAierveidp t e++++vig+e        
  lcl|FitnessBrowser__Dino:3608276 390 ELVLIVDVGTNAEILLGNRDRVLACSSPTGPAFEGAQISSGQRAAPGAIERVEIDPVTKEPRFRVIGCELwsddpgf 466
                                       679****************************************************************999999**** PP

                        RACo_C_ter  71 ........pkGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvlaeesetekdivitekDi 137
                                               ++GicGsGii+++ae+  ag++d +g +       ++r  +e +t++yvl++++  + ++ i +t+ Di
  lcl|FitnessBrowser__Dino:3608276 467 aeataatgITGICGSGIIEAVAEMRMAGLLDASGLIGGPEqtGTPRSIAEGRTYSYVLQDDR-PAGGSLIAVTQGDI 542
                                       ************************************87652256677777788888886654.455679******** PP

                        RACo_C_ter 138 delirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAraalls 214
                                       ++++ ak+A+yag+++L++e+g  v+ +d+v+laGafG++i +++A+++G++Pd +l+kv+++GN++++gAr+al+s
  lcl|FitnessBrowser__Dino:3608276 543 RAIQLAKSALYAGARLLMDEMG--VDTVDRVTLAGAFGAHISPKHAMVLGMIPDAPLDKVTSAGNAAGTGARMALCS 617
                                       ********************99..9**************************************************** PP

                        RACo_C_ter 215 reareeleeiarkityielavekkFmeefvaalflphtdlelfps 259
                                       r+ar+e+e+ ++kit++e+a e++F+e+fvaa ++ph ++ +f +
  lcl|FitnessBrowser__Dino:3608276 618 RAARAEIEQTVSKITKVETAIEPRFQEHFVAANAIPHATA-PFAH 661
                                       *************************************776.6765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (690 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: 17.15
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
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