Alignments for a candidate for ramA in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Sinorhizobium fredii NGR234

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate YP_002826366.1 NGR_c18490 electron transfer protein

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



>NCBI__GCF_000018545.1:YP_002826366.1
          Length = 691

 Score =  771 bits (1991), Expect = 0.0
 Identities = 398/690 (57%), Positives = 495/690 (71%), Gaps = 7/690 (1%)

Query: 8   EISTETATDPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQIT 67
           EI T         PLV+F PSGKRGRFP+GTP+L AAR LGV ++SVCGGR  C +CQ++
Sbjct: 8   EIETNMTEAAQKKPLVLFMPSGKRGRFPIGTPILDAARSLGVYVESVCGGRATCGRCQVS 67

Query: 68  PSYGEFSKHGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQV 127
              G F+KH +  +++ ++     EQRY   R L DGRRL C AQ+ GD+VIDVP ++ +
Sbjct: 68  VQEGNFAKHKIVSSNEHISPVGPKEQRYASVRELPDGRRLSCSAQILGDLVIDVPQDTVI 127

Query: 128 HRQVVRKRAEARDITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLH 187
           + QVVRK A  R I  N + +L YVEVEEPDMHKP GD++RL   L+  W  K +    H
Sbjct: 128 NAQVVRKAATDRVIERNAAVQLCYVEVEEPDMHKPLGDLDRLKAVLEKDWGWKDLLIAPH 187

Query: 188 ILSVLQPALRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLC 247
           ++  LQ  LRKG W VT A+H   ++  P I+ + PG  +   YG+A D+GSTTIA HL 
Sbjct: 188 LIPQLQGILRKGNWAVTAAIHRDMDSSRPFIVGLSPGL-KNEAYGVACDIGSTTIAMHLV 246

Query: 248 DLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEA 307
            L +G +VASSG  NPQIRFGEDLMSRVSY MMN  G + MT+AVRE +N L  ++ AE 
Sbjct: 247 SLLSGRIVASSGASNPQIRFGEDLMSRVSYVMMNPDGREAMTKAVREAVNGLIGKVCAEG 306

Query: 308 EIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARV 367
           EID+  I+D V V NP+MHHLFLGIDP ELGQAPFALA S AL   A E+D+ ++  AR+
Sbjct: 307 EIDRHDILDMVVVGNPIMHHLFLGIDPTELGQAPFALAVSGALQYWAHEIDIEVNRGARL 366

Query: 368 YLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAF 427
           Y+LPCIAGHVGADAA   LSE P + + ++L+VDVGTNAEI+LGNK++V+A SSPTGPAF
Sbjct: 367 YMLPCIAGHVGADAAGATLSEGPHRQDKMMLLVDVGTNAEIVLGNKERVVAASSPTGPAF 426

Query: 428 EGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSG 487
           EGA+ISSGQRAAPGAIERV I+PET EPRFRVIG D WSDE+GFA A A TG+TGICGS 
Sbjct: 427 EGAEISSGQRAAPGAIERVRIDPETLEPRFRVIGVDKWSDEEGFAEAAAATGVTGICGSA 486

Query: 488 IIEAIAEMRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDI 547
           IIE +AEM + G++   G++  A    + R + +GRT +YLL DG     P ITVT  DI
Sbjct: 487 IIEVVAEMYLTGIISQDGVVDGAMAARSPRIVPNGRTFSYLLHDGE----PKITVTQNDI 542

Query: 548 RAIQMAKAALYSGARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTS 607
           RAIQ+AKAALY+G +LLM+K G++ VD +  AGAFG+ I  K+AMVLG+IPDC L +V +
Sbjct: 543 RAIQLAKAALYAGIKLLMEKQGVEHVDTIRFAGAFGSFIDPKYAMVLGLIPDCDLAEVKA 602

Query: 608 AGNAAGTGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPIL 667
            GNAAGTGA +ALLN   R EIE TV++IEKIETA+E +FQEHFVNA A+PN  + FP L
Sbjct: 603 VGNAAGTGALMALLNRGHRREIEETVRKIEKIETALESKFQEHFVNAMAMPNKVDAFPKL 662

Query: 668 SSIVTLPEANFNTGGGDGNEVGGRRRRRRR 697
           + +VTLPE        DG E GGRRRRR R
Sbjct: 663 AEVVTLPER--KVPADDGGEGGGRRRRRSR 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: 1149
Number of extensions: 41
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: 691
Length adjustment: 39
Effective length of query: 659
Effective length of database: 652
Effective search space:   429668
Effective search space used:   429668
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 YP_002826366.1 NGR_c18490 (electron transfer 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.29327.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.3e-95  304.6   0.7    3.8e-95  303.9   0.7    1.3  1  lcl|NCBI__GCF_000018545.1:YP_002826366.1  NGR_c18490 electron transfer pro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002826366.1  NGR_c18490 electron transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.9   0.7   3.8e-95   3.8e-95       1     260 [.     394     662 ..     394     663 .. 0.97

  Alignments for each domain:
  == domain 1  score: 303.9 bits;  conditional E-value: 3.8e-95
                                RACo_C_ter   1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvigne 69 
                                               +++ll+D+GTNaEivlgnk++++aas+++GPA+EG+ei++G+rAapgAierv+idpetle++++vig +
  lcl|NCBI__GCF_000018545.1:YP_002826366.1 394 KMMLLVDVGTNAEIVLGNKERVVAASSPTGPAFEGAEISSGQRAAPGAIERVRIDPETLEPRFRVIGVD 462
                                               589****************************************************************99 PP

                                RACo_C_ter  70 k...............pkGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvla 121
                                               k               ++GicGs+ii+++ae++++gii+++g ++  +  +s+ri  + +t +y+l++ 
  lcl|NCBI__GCF_000018545.1:YP_002826366.1 463 KwsdeegfaeaaaatgVTGICGSAIIEVVAEMYLTGIISQDGVVDGAMaaRSPRIVPNGRTFSYLLHDG 531
                                               999*****************************************99877799**************998 PP

                                RACo_C_ter 122 eesetekdivitekDidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllP 190
                                               e      +i++t++Di++++ akaA+yag+k+L+e+ g  ve++d++ +aGafGs+id+++A+++Gl+P
  lcl|NCBI__GCF_000018545.1:YP_002826366.1 532 E-----PKITVTQNDIRAIQLAKAALYAGIKLLMEKQG--VEHVDTIRFAGAFGSFIDPKYAMVLGLIP 593
                                               7.....58******************************..9**************************** PP

                                RACo_C_ter 191 dlelekvkqvGNtslagAraallsreareeleeiarkityielavekkFmeefvaalflphtdlelfps 259
                                               d++l++vk+vGN++++gA +all+r +r+e+ee +rki++ie+a e+kF+e+fv+a+++p+ ++++fp+
  lcl|NCBI__GCF_000018545.1:YP_002826366.1 594 DCDLAEVKAVGNAAGTGALMALLNRGHRREIEETVRKIEKIETALESKFQEHFVNAMAMPN-KVDAFPK 661
                                               *************************************************************.7789997 PP

                                RACo_C_ter 260 v 260
                                               +
  lcl|NCBI__GCF_000018545.1:YP_002826366.1 662 L 662
                                               6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (691 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: 18.32
//
[ok]

This GapMind analysis is from Apr 10 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