Alignments for a candidate for ramA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Sinorhizobium meliloti 1021

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate SMc04347 SMc04347 hypothetical protein

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



>FitnessBrowser__Smeli:SMc04347
          Length = 683

 Score =  761 bits (1966), Expect = 0.0
 Identities = 389/682 (57%), Positives = 491/682 (71%), Gaps = 7/682 (1%)

Query: 16  DPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSK 75
           D  + PLV+F PSGKRGRFPVGTP+L AAR LGV ++SVCGGR  C +CQ++   G F+K
Sbjct: 8   DEKNDPLVLFMPSGKRGRFPVGTPILDAARSLGVYVESVCGGRATCGRCQVSVQEGNFAK 67

Query: 76  HGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKR 135
           H +  + D ++     EQRY   R L DGRRL C +Q+ GD+VIDVP ++ ++ QVVRK 
Sbjct: 68  HKIVSSSDHISPIGPKEQRYASVRELPDGRRLSCSSQILGDLVIDVPQDTVINAQVVRKA 127

Query: 136 AEARDITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPA 195
           A  R I  N + +L YVE++EPDMHKP GD++R+   L+  W  K +    H++  +Q  
Sbjct: 128 ASDRVIERNAAVQLCYVEIDEPDMHKPLGDLDRMKAVLEKDWGWKDLLIAPHLIPQVQGI 187

Query: 196 LRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVV 255
           LRKG W VT A+H   ++  P I+ +WPG  +   YG+A D+GSTTIA HL  L +G +V
Sbjct: 188 LRKGNWAVTAAIHRDMDSSRPFIVALWPGL-KNEAYGVACDIGSTTIAMHLVSLLSGRIV 246

Query: 256 ASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIV 315
           ASSG  NPQIRFGEDLMSRVSY MMN  G + MT+AVRE +N L  ++ AE E+D+  I+
Sbjct: 247 ASSGTSNPQIRFGEDLMSRVSYVMMNPDGREAMTKAVREALNGLIGKVCAEGEVDRHDIL 306

Query: 316 DAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAG 375
           D V V NP+MHHLFLGIDP ELGQAPFALA S AL   A E+D+ ++  AR+Y+LPCIAG
Sbjct: 307 DMVVVANPIMHHLFLGIDPTELGQAPFALAVSGALQYWAHEIDIEVNRGARLYMLPCIAG 366

Query: 376 HVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSG 435
           HVGADAA   LSE P + + ++L+VDVGTNAEI+LGN+++V+A SSPTGPAFEGA+ISSG
Sbjct: 367 HVGADAAGATLSEGPHRQDKMMLLVDVGTNAEIVLGNRERVVAASSPTGPAFEGAEISSG 426

Query: 436 QRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEM 495
           QRAAPGAIERV I+PET EPRFRVIG D WS+E+GFA A A  G+TGICGS IIE +AEM
Sbjct: 427 QRAAPGAIERVRIDPETLEPRFRVIGVDKWSNEEGFAEAAAAVGVTGICGSAIIEVVAEM 486

Query: 496 RMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKA 555
            + G++   G++  A    + R I +GRT +YLL     EG   ITVT  DIRAIQ+AK+
Sbjct: 487 YLTGIISQDGVVDGAMVAKSPRIIPNGRTFSYLLH----EGEQRITVTQNDIRAIQLAKS 542

Query: 556 ALYSGARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTG 615
           ALY+G +LLM+K G+D VD +  AGAFG+ I  K+AMVLG+IPDC L +V + GNAAGTG
Sbjct: 543 ALYAGIKLLMEKQGVDHVDTIRFAGAFGSFIDPKYAMVLGLIPDCDLTEVKAVGNAAGTG 602

Query: 616 ARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIVTLPE 675
           A +ALLN   R EIE TV++IEKIETA+E +FQEHFVNA A+PN  + FP L+ +VTLP 
Sbjct: 603 ALMALLNRGHRREIEQTVRKIEKIETALESKFQEHFVNAMAMPNKVDAFPKLAEVVTLPA 662

Query: 676 ANFNTGGGDGNEVGGRRRRRRR 697
               T   DG E  GRRRRR R
Sbjct: 663 RKSLT--DDGGEGSGRRRRRSR 682


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: 1123
Number of extensions: 34
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: 683
Length adjustment: 39
Effective length of query: 659
Effective length of database: 644
Effective search space:   424396
Effective search space used:   424396
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 SMc04347 SMc04347 (hypothetical 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.12705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      5e-95  303.5   0.8    7.4e-95  303.0   0.8    1.2  1  lcl|FitnessBrowser__Smeli:SMc04347  SMc04347 hypothetical protein


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04347  SMc04347 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.0   0.8   7.4e-95   7.4e-95       1     260 [.     386     654 ..     386     655 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.0 bits;  conditional E-value: 7.4e-95
                          RACo_C_ter   1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek..... 70 
                                         +++ll+D+GTNaEivlgn+++++aas+++GPA+EG+ei++G+rAapgAierv+idpetle++++vig +k     
  lcl|FitnessBrowser__Smeli:SMc04347 386 KMMLLVDVGTNAEIVLGNRERVVAASSPTGPAFEGAEISSGQRAAPGAIERVRIDPETLEPRFRVIGVDKwsnee 460
                                         589****************************************************************999999** PP

                          RACo_C_ter  71 ..........pkGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvlaeesetekdivit 133
                                                   ++GicGs+ii+++ae++++gii+++g ++  +  ks+ri  + +t +y+l++ e     ++i++t
  lcl|FitnessBrowser__Smeli:SMc04347 461 gfaeaaaavgVTGICGSAIIEVVAEMYLTGIISQDGVVDGAMvaKSPRIIPNGRTFSYLLHEGE-----QRITVT 530
                                         **************************************99988899**************9987.....69**** PP

                          RACo_C_ter 134 ekDidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagA 208
                                         ++Di++++ ak+A+yag+k+L+e+ g  v+++d++ +aGafGs+id+++A+++Gl+Pd++l +vk+vGN++++gA
  lcl|FitnessBrowser__Smeli:SMc04347 531 QNDIRAIQLAKSALYAGIKLLMEKQG--VDHVDTIRFAGAFGSFIDPKYAMVLGLIPDCDLTEVKAVGNAAGTGA 603
                                         **************************..9********************************************** PP

                          RACo_C_ter 209 raallsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsv 260
                                          +all+r +r+e+e+ +rki++ie+a e+kF+e+fv+a+++p+ ++++fp++
  lcl|FitnessBrowser__Smeli:SMc04347 604 LMALLNRGHRREIEQTVRKIEKIETALESKFQEHFVNAMAMPN-KVDAFPKL 654
                                         *******************************************.77899976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (683 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: 00:00:00.01
# Mc/sec: 17.11
//
[ok]

This GapMind analysis is from Apr 09 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