Alignments for a candidate for aroA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Sinorhizobium meliloti 1021

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate SMc00333 SMc00333 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>FitnessBrowser__Smeli:SMc00333
          Length = 455

 Score =  837 bits (2163), Expect = 0.0
 Identities = 422/448 (94%), Positives = 438/448 (97%)

Query: 1   MSHGLSPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           MSHG +PRPATA+KS+DLKGT+RIPGDKSISHRSFMFGGLA+GETRITGLLEGEDVINTG
Sbjct: 1   MSHGSNPRPATARKSSDLKGTLRIPGDKSISHRSFMFGGLAAGETRITGLLEGEDVINTG 60

Query: 61  KAMQAMGAKIRKEGDTWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFI 120
           KAMQAMGA+IRKEGDTWII+GVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFI
Sbjct: 61  KAMQAMGARIRKEGDTWIIDGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFI 120

Query: 121 GDASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAV 180
           GDASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAV
Sbjct: 121 GDASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAV 180

Query: 181 LLAGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVID 240
           LLAGLNTPGITTV+EPVMTRDHTEKMLQGFGANL+VETD  GVRTIRLEGRGKLTGQVID
Sbjct: 181 LLAGLNTPGITTVVEPVMTRDHTEKMLQGFGANLTVETDAEGVRTIRLEGRGKLTGQVID 240

Query: 241 VPGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGED 300
           VPGDPSSTAFPLVA L+VPGSD+TILNVLMNPTRTGLILTLQEMGANIEVMN RLAGGED
Sbjct: 241 VPGDPSSTAFPLVAGLIVPGSDITILNVLMNPTRTGLILTLQEMGANIEVMNKRLAGGED 300

Query: 301 VADLRVRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLSA 360
           VADLRVR+SELKGVTVPE+RAPSMIDEYPVLAVAAAFAEG TVMNGL+ELRVKESDRLSA
Sbjct: 301 VADLRVRHSELKGVTVPEDRAPSMIDEYPVLAVAAAFAEGTTVMNGLEELRVKESDRLSA 360

Query: 361 VADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASEHP 420
           VADGLKLNGVDCDEGEASLVVRGRPGGKGLG  +GGQVKTHLDHRIAMSFLV+GLASEHP
Sbjct: 361 VADGLKLNGVDCDEGEASLVVRGRPGGKGLGKISGGQVKTHLDHRIAMSFLVMGLASEHP 420

Query: 421 VTVDDATMIATSFPEFMDLMTGLGATIE 448
           VTVDDATMIATSFPEFM LMTGLGA IE
Sbjct: 421 VTVDDATMIATSFPEFMGLMTGLGAKIE 448


Lambda     K      H
   0.316    0.135    0.385 

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: 913
Number of extensions: 29
Number of successful extensions: 1
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: 448
Length of database: 455
Length adjustment: 33
Effective length of query: 415
Effective length of database: 422
Effective search space:   175130
Effective search space used:   175130
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 SMc00333 SMc00333 (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.19758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.7e-137  442.4   0.0   8.7e-137  442.2   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00333  SMc00333 3-phosphoshikimate 1-ca


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00333  SMc00333 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.2   0.0  8.7e-137  8.7e-137       1     414 [.      20     445 ..      20     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 442.2 bits;  conditional E-value: 8.7e-137
                           TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lkepeael 73 
                                         g ++ipg+KSishR++++++La get++t+lL++eD+++t +a++++Ga++++e+++++i+gvg+  l  pea l
  lcl|FitnessBrowser__Smeli:SMc00333  20 GTLRIPGDKSISHRSFMFGGLAAGETRITGLLEGEDVINTGKAMQAMGARIRKEGDTWIIDGVGNgaLLAPEAPL 94 
                                         679************************************************************99999******* PP

                           TIGR01356  74 dlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivel 147
                                         d+gn+Gt  Rl++g++ ++++++++ gd sl kRP++r++++Lre+g++++s+e+ ++lP++++gp  + +i++ 
  lcl|FitnessBrowser__Smeli:SMc00333  95 DFGNAGTGCRLTMGLVGVYDFDSTFIGDASLTKRPMGRVLDPLREMGVQVKSAEG-DRLPVTLRGPkTPNPITYR 168
                                         ****************************************************995.7*********5555***** PP

                           TIGR01356 148 sgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede..rkivvkggqkykqkev 220
                                          ++aS+Q+ksa+lla+   l++ ++++v e++++r+++e++L+ +++   +ve + e  r+i+++g +k + + +
  lcl|FitnessBrowser__Smeli:SMc00333 169 VPMASAQVKSAVLLAG---LNTPGITTVVEPVMTRDHTEKMLQGFGAN-LTVETDAEgvRTIRLEGRGKLTGQVI 239
                                         ****************...89999*********************977.7888777788**********55555* PP

                           TIGR01356 221 evegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegaskl 286
                                         +v+gD+Ss+af+l+a++i ++ ++t+ n+++n+t+++  +i +L+emGa++ev ++r        d++v+ +s+l
  lcl|FitnessBrowser__Smeli:SMc00333 240 DVPGDPSSTAFPLVAGLIVPGsDITILNVLMNPTRTG--LILTLQEMGANIEVMNKRlaggedvaDLRVR-HSEL 311
                                         *********************9***************..777****************************.689* PP

                           TIGR01356 287 kgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkk. 359
                                         kgv+v + +++s+iDe+p+lav+aafAeg+t+++++eelRvkEsdR++a+a+ L+  Gv+++e+e +l+++G+  
  lcl|FitnessBrowser__Smeli:SMc00333 312 KGVTVpEDRAPSMIDEYPVLAVAAAFAEGTTVMNGLEELRVKESDRLSAVADGLKLNGVDCDEGEASLVVRGRPg 386
                                         *****9999***************************************************************999 PP

                           TIGR01356 360 ....kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                              +++g++v+t+ DHRiam++ v+gla e++v+++da ++a+sfPeF+ ++  lga
  lcl|FitnessBrowser__Smeli:SMc00333 387 gkglGKISGGQVKTHLDHRIAMSFLVMGLASEHPVTVDDATMIATSFPEFMGLMTGLGA 445
                                         9899999***********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (455 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.85
//
[ok]

This GapMind analysis is from Apr 09 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