Alignments for a candidate for aroA in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Rhodospirillum rubrum ATCC 11170

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011388048.1 RRU_RS01545 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9R4E4
         (455 letters)



>NCBI__GCF_000013085.1:WP_011388048.1
          Length = 451

 Score =  481 bits (1237), Expect = e-140
 Identities = 265/447 (59%), Positives = 306/447 (68%), Gaps = 9/447 (2%)

Query: 8   RPATARKSSGLSGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKAMQAMG 67
           RP  A +S+ LSG +R+PGDKSISHR+ M GGLA G T I GLLEGEDVI T  AM+AMG
Sbjct: 8   RPLRAHRSTPLSGRIRVPGDKSISHRALMLGGLAVGRTEIRGLLEGEDVIATAHAMEAMG 67

Query: 68  ARIRKE-----GDTWIIDGVGNGGLLAPEAPLDFGNAATGCRLTMGLVGVYDFDSTFIGD 122
           ARI ++        W +DGVG GGL  P   LD GNA TG RL MGL+  +D  +   GD
Sbjct: 68  ARIDRQETADGAGVWTVDGVGVGGLAEPADVLDMGNAGTGARLLMGLLATHDLTAILTGD 127

Query: 123 ASLTKRPMGRVLNPLREMGVQVKSEDGDRLPVTLRGPKTPTPITYRVPMASAQVKSAVLL 182
           ASL  RPM RV +PL   G       G RLP+ +RG  TP P++YRVP+ SAQVKSAVLL
Sbjct: 128 ASLRGRPMKRVTDPLALFGASFVGRSGGRLPMAVRGTATPLPVSYRVPVPSAQVKSAVLL 187

Query: 183 AGLNTPGITTVIEPIMTRDHTEKMLQGFGANLTVETDADGVRTIRLEGRGKLTGQVIDVP 242
           AGLNTPG TTVIEP+ TRDHTE+ML  FGA L +  D  G  TI L G+ +L    ++VP
Sbjct: 188 AGLNTPGETTVIEPVATRDHTERMLGHFGAALRLGRDDQGATTITLTGQPELRAAPVEVP 247

Query: 243 GDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGADIEVINPRLAGGEDVA 302
            DPSS AFPLVAA+LVP S VT+  V MNP R GLI TL+EMGADI + +PR+  GE VA
Sbjct: 248 ADPSSAAFPLVAAVLVPESHVTLAGVGMNPQRIGLIDTLREMGADILIRDPRIEAGEPVA 307

Query: 303 DLRVRSSTLKGVTVPEDRAPSMIDEYPILAVAAAFAEGATVMNGLEELRVKESDRLSAVA 362
           DL VR+S L G+ VP  RAPSMIDEYPILAVAAA A G T M+GL ELRVKESDRLSAVA
Sbjct: 308 DLEVRASALTGIEVPAARAPSMIDEYPILAVAAACARGTTRMHGLGELRVKESDRLSAVA 367

Query: 363 NGLKLNGVDCDEGETSLVVRGRPDGKGLGNASGAAVATHLDHRIAMSFLVMGLVSENPVT 422
            GL   GVD      +L+V     GKG     GA VA +LDHRI M+FLV+GLVS   VT
Sbjct: 368 TGLAACGVDVTVDGDTLIVH----GKGTVPKGGATVAVNLDHRIGMAFLVLGLVSAEAVT 423

Query: 423 VDDATMIATSFPEFMDLMAGLGAKIEL 449
           +DD   I TSFP F+ LM GLGA I L
Sbjct: 424 IDDGRAIDTSFPGFVTLMTGLGAPISL 450


Lambda     K      H
   0.316    0.135    0.380 

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: 745
Number of extensions: 40
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: 455
Length of database: 451
Length adjustment: 33
Effective length of query: 422
Effective length of database: 418
Effective search space:   176396
Effective search space used:   176396
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: 51 (24.3 bits)

Align candidate WP_011388048.1 RRU_RS01545 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.2690368.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-121  392.1   0.0   1.6e-121  392.0   0.0    1.0  1  NCBI__GCF_000013085.1:WP_011388048.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013085.1:WP_011388048.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.0   0.0  1.6e-121  1.6e-121       1     414 [.      20     446 ..      20     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 392.0 bits;  conditional E-value: 1.6e-121
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee....keelviegvgg..l 66 
                                           g+i++pg+KSishRal+l++La g+t++++lL++eD++at +a++++Ga++  +e     ++++++gvg   l
  NCBI__GCF_000013085.1:WP_011388048.1  20 GRIRVPGDKSISHRALMLGGLAVGRTEIRGLLEGEDVIATAHAMEAMGARIDrQEtadgAGVWTVDGVGVggL 92 
                                           79*************************************************85333223468****998888* PP

                             TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp 139
                                           +ep ++ld+gn+Gt aRll+g+la+++ + +ltgd sl+ RP++r++++L  +ga++  ++  g+lP+a++g+
  NCBI__GCF_000013085.1:WP_011388048.1  93 AEPADVLDMGNAGTGARLLMGLLATHDLTAILTGDASLRGRPMKRVTDPLALFGASFVGRS-GGRLPMAVRGT 164
                                           ***********************************************************99.59********* PP

                             TIGR01356 140 .lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede..rkivv 209
                                             ++++++  +  S+Q+ksa+lla+   l++ ++++v+e++ +r+++e++L  ++++  ++ ++d+  ++i++
  NCBI__GCF_000013085.1:WP_011388048.1 165 aTPLPVSYRVPVPSAQVKSAVLLAG---LNTPGETTVIEPVATRDHTERMLGHFGAA-LRLGRDDQgaTTITL 233
                                           7888*********************...88899999999****************98.999999998888888 PP

                             TIGR01356 210 kggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr..... 276
                                           +g+ + +   vev++D+SsAaf+l+aa++ +e +vt+ ++g+n+++ +  +i++L+emGad+ + + r     
  NCBI__GCF_000013085.1:WP_011388048.1 234 TGQPELRAAPVEVPADPSSAAFPLVAAVLVPEsHVTLAGVGMNPQRIG--LIDTLREMGADILIRDPRieage 304
                                           8888855556**********************9***************..888************99999*** PP

                             TIGR01356 277 ...dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGve 345
                                              d+ev+ as l g++v  ++++s+iDe+p+lav+aa+A+g+tr++++ elRvkEsdR++a+a+ L++ Gv+
  NCBI__GCF_000013085.1:WP_011388048.1 305 pvaDLEVR-ASALTGIEVpAARAPSMIDEYPILAVAAACARGTTRMHGLGELRVKESDRLSAVATGLAACGVD 376
                                           ********.899******88***************************************************** PP

                             TIGR01356 346 veeledgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           v++  d l+++Gk +  kg a+v    DHRi ma+ vlgl+ ++ v+i+d  ++++sfP F+ ++  lga
  NCBI__GCF_000013085.1:WP_011388048.1 377 VTVDGDTLIVHGKGTVPKGgATVAVNLDHRIGMAFLVLGLVSAEAVTIDDGRAIDTSFPGFVTLMTGLGA 446
                                           *************8666666999999***************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (451 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: 00:00:00.00
# Mc/sec: 19.32
//
[ok]

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