Alignments for a candidate for ramA in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Phyllobacterium endophyticum PEPV15

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_106718622.1 CU100_RS18340 DUF4445 domain-containing protein

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



>NCBI__GCF_003010935.1:WP_106718622.1
          Length = 675

 Score =  766 bits (1977), Expect = 0.0
 Identities = 384/669 (57%), Positives = 491/669 (73%), Gaps = 5/669 (0%)

Query: 27  PSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHGVTVADDALT 86
           PSGKRGRF VGTP+L AAR LGV ++SVCGGRGIC +CQ+    G F+KHG+T ++D ++
Sbjct: 2   PSGKRGRFAVGTPILEAARTLGVYVESVCGGRGICGRCQVEVQEGRFAKHGITSSNDHIS 61

Query: 87  EWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEARDITMNPS 146
           E+   EQRY +KR L  GRRL C A + GD+V+DVP + Q++ QVVRK  + R I  NP+
Sbjct: 62  EFGPKEQRYAEKRDLKQGRRLSCSATILGDLVVDVPQDVQINAQVVRKDVDTRVIERNPA 121

Query: 147 TRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLKGVKTDLHILSVLQPALRKGGWKVTVA 206
            R+ YVEVEEPDMHKP GD++RL  AL+ +W ++ +  D ++L+ +Q  LRKG W VT A
Sbjct: 122 VRMCYVEVEEPDMHKPLGDLDRLKIALENEWGVRNLNVDAYLLANVQQILRKGEWGVTAA 181

Query: 207 VHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVASSGIMNPQIR 266
           +H  +E   P ++ +WPG  +   YG+A D+GSTTIA HL  L +   +AS+G  NPQIR
Sbjct: 182 IHHDEETDRPTMIGLWPGL-KNEAYGIACDIGSTTIAMHLSSLLSVRTIASAGTSNPQIR 240

Query: 267 FGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVFVCNPVMH 326
           FGEDLMSRVSY MMN  G + MT AVRE +N L  ++  E  + +  I+DAVFV NP+MH
Sbjct: 241 FGEDLMSRVSYVMMNPDGREGMTLAVREAINGLIDKVCLEGGVAREDILDAVFVGNPIMH 300

Query: 327 HLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGADAAAVAL 386
           HLFLGIDP ELG APFALA S A+ L++ ++ L ++P  RVY+LPCIAGHVGADAAA  L
Sbjct: 301 HLFLGIDPTELGGAPFALAVSGAVHLKSSDIGLPMNPGTRVYMLPCIAGHVGADAAAATL 360

Query: 387 SEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAAPGAIERV 446
           +E P + ++++L+VDVGTNAEI+LGN+ + +A SSPTGPAFEGA+IS GQRAAPGAIERV
Sbjct: 361 AEGPHRQDEMMLLVDVGTNAEIVLGNRQRTVAASSPTGPAFEGAEISGGQRAAPGAIERV 420

Query: 447 EINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEMRMAGLLDASGL 506
            I+P T EP+FRVIG++ WSDE GF  AV  +GITGICGS IIE IAEM ++G++   G+
Sbjct: 421 RIDPVTLEPKFRVIGTEKWSDEPGFEEAVQASGITGICGSAIIEVIAEMYLSGIISEDGV 480

Query: 507 IGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKAALYSGARLLMD 566
           +       + R + +GRT +YLL +GS    PTIT+T  D+RAIQ+AKAALY+G +LLMD
Sbjct: 481 VDGTLSVKSPRVMANGRTFSYLLHEGS----PTITITQNDVRAIQLAKAALYAGVKLLMD 536

Query: 567 KFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIALLNTEAR 626
           K GID VD++  AGAFG+ I  K+AMVLG+IPDC LDKV + GNAAGTGAR+ALLN   R
Sbjct: 537 KLGIDHVDQIRFAGAFGSFIDPKYAMVLGLIPDCDLDKVQAVGNAAGTGARMALLNRNYR 596

Query: 627 SEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIVTLPEANFNTGGGDGN 686
            EIEATV +IEKIETA+EP+FQEHFV A A+PN  +PFP LS  VTLP     +  G   
Sbjct: 597 REIEATVTRIEKIETALEPKFQEHFVYAMAMPNKIDPFPKLSMAVTLPPRKNVSEDGVAG 656

Query: 687 EVGGRRRRR 695
           +   RRR R
Sbjct: 657 DASPRRRSR 665


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: 1162
Number of extensions: 43
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: 675
Length adjustment: 39
Effective length of query: 659
Effective length of database: 636
Effective search space:   419124
Effective search space used:   419124
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 WP_106718622.1 CU100_RS18340 (DUF4445 domain-containing 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.461648.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.2e-95  302.8   0.5    1.5e-94  302.0   0.1    1.6  2  NCBI__GCF_003010935.1:WP_106718622.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106718622.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       0.2       0.2      72      97 ..      33      58 ..      26      80 .. 0.62
   2 !  302.0   0.1   1.5e-94   1.5e-94       1     260 [.     369     637 ..     369     638 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.2
                            RACo_C_ter 72 kGicGsGiidliaelleagiidkkgk 97
                                          +GicG   +++ +  + +  i+++  
  NCBI__GCF_003010935.1:WP_106718622.1 33 RGICGRCQVEVQEGRFAKHGITSSND 58
                                          68888888888776665544444333 PP

  == domain 2  score: 302.0 bits;  conditional E-value: 1.5e-94
                            RACo_C_ter   1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek... 70 
                                           e++ll+D+GTNaEivlgn+++ +aas+++GPA+EG+ei+ G+rAapgAierv+idp tle++++vig ek   
  NCBI__GCF_003010935.1:WP_106718622.1 369 EMMLLVDVGTNAEIVLGNRQRTVAASSPTGPAFEGAEISGGQRAAPGAIERVRIDPVTLEPKFRVIGTEKwsd 441
                                           799*****************************************************************999** PP

                            RACo_C_ter  71 ............pkGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvlaeesetekd 129
                                                       ++GicGs+ii++iae++++gii+++g ++ +l  ks+r+ ++ +t +y+l++ +       
  NCBI__GCF_003010935.1:WP_106718622.1 442 epgfeeavqasgITGICGSAIIEVIAEMYLSGIISEDGVVDGTLsvKSPRVMANGRTFSYLLHEGS-----PT 509
                                           ****************************************99877799**************9876.....47 PP

                            RACo_C_ter 130 ivitekDidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGN 202
                                           i+it++D+++++ akaA+yagvk+L++++g  ++++d++ +aGafGs+id+++A+++Gl+Pd++l+kv++vGN
  NCBI__GCF_003010935.1:WP_106718622.1 510 ITITQNDVRAIQLAKAALYAGVKLLMDKLG--IDHVDQIRFAGAFGSFIDPKYAMVLGLIPDCDLDKVQAVGN 580
                                           ****************************99..99*************************************** PP

                            RACo_C_ter 203 tslagAraallsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsv 260
                                           ++++gAr+all+r+ r+e+e+ +++i++ie+a e+kF+e+fv a+++p+ ++++fp++
  NCBI__GCF_003010935.1:WP_106718622.1 581 AAGTGARMALLNRNYRREIEATVTRIEKIETALEPKFQEHFVYAMAMPN-KIDPFPKL 637
                                           *************************************************.88899986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (675 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.69
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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 original 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