Alignments for a candidate for aroA in Salinicoccus carnicancri Crm

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Salinicoccus carnicancri Crm

Align 5-enolpyruvoylshikimate-3-phosphate synthase (EC 2.5.1.19) (characterized)
to candidate WP_017548940.1 C792_RS0107955 3-phosphoshikimate 1-carboxyvinyltransferase

Query= metacyc::AROEBACSU-MONOMER
         (428 letters)



>NCBI__GCF_000330705.1:WP_017548940.1
          Length = 428

 Score =  339 bits (870), Expect = 8e-98
 Identities = 196/428 (45%), Positives = 261/428 (60%), Gaps = 4/428 (0%)

Query: 1   MKRDKVQTLHGEIHIPGDKSISHRSVMFGALAAGTTTVKNFLPGADCLSTIDCFRKMGVH 60
           MK+   +T  G + +PGDKSI+HRS+M  ALA G T +   L   D   T++  R +G  
Sbjct: 1   MKQLLNRTFEGTLRVPGDKSITHRSLMLAALAEGRTEIHLPLKSEDTYRTMEIMRAIGAD 60

Query: 61  IEQSSSDVVIHGKGIDALKEPESLLDVGNSGTTIRLMLGILAGRPFYSAVAGDESIAKRP 120
           I +S    ++  +G   L  P   L  GNSGTT RL++G+LAG    +  +GD+SI +RP
Sbjct: 61  ITESGDIWIVESRGHAHLHSPAGPLYTGNSGTTSRLIIGLLAGLGLEAEFSGDDSINRRP 120

Query: 121 MKRVTEPLKKMGAKIDGRAGGEFTPLSVSGASLKGIDYVSPVASAQIKSAVLLAGLQAEG 180
           M RV  PL  MGA I  +   ++ P+ +    LK IDY  P+ASAQ+KSAVLLAGL AEG
Sbjct: 121 MDRVQRPLLDMGADIRLK-DEKYPPVHIYPKPLKAIDYDMPIASAQVKSAVLLAGLFAEG 179

Query: 181 TTTVTEPHKSRDHTERMLSAFGVKLSEDQTSVSIAGGQKLTAADIFVPGDISSAAFFLAA 240
           TT V E   SRDH+E M+  FG +LS     +S+ GG+ LT+AD+ VPGDISSAAF LA 
Sbjct: 180 TTVVRESSPSRDHSEIMMKQFGAELSSKDGVISLTGGKNLTSADVTVPGDISSAAFPLAL 239

Query: 241 GAMVPNSRIVLKNVGLNPTRTGIIDVLQNMGAKLEIKPSADSGAEPYGDLIIE-TSSLKA 299
             + P + I ++NV LNPTR+GI++VL+ M A +EI+     G E  G++    T  L+ 
Sbjct: 240 AILKPGTSITIENVSLNPTRSGILEVLEMMDANIEIETLPGDG-EAIGNITASYTPELRG 298

Query: 300 VEIGGDIIPRLIDEIPIIALLATQAEGTTVIKDAAELKVKETNRIDTVVSELRKLGAEIE 359
            +I G+IIPRLIDEIPI+ALLA  +  +  + DA EL+ KET+RI  VV EL K G   E
Sbjct: 299 FDISGEIIPRLIDEIPILALLAAYSNESCTVSDAGELRFKETDRIRAVVDELSKFGIRFE 358

Query: 360 PTADGMKVY-GKQTLKGGAAVSSHGDHRIGMMLGIASCITEEPIEIEHTDAIHVSYPTFF 418
              DG  V  G+     G AV  + DHRI MML I S +++ P+ I+ T AI +SYP F 
Sbjct: 359 EKEDGFTVLPGEIEPAAGTAVKGYHDHRIIMMLIIFSIVSDTPLNIDDTSAIDISYPGFI 418

Query: 419 EHLNKLSK 426
             L  L K
Sbjct: 419 NDLESLRK 426


Lambda     K      H
   0.315    0.133    0.368 

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: 477
Number of extensions: 21
Number of successful extensions: 4
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: 428
Length of database: 428
Length adjustment: 32
Effective length of query: 396
Effective length of database: 396
Effective search space:   156816
Effective search space used:   156816
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_017548940.1 C792_RS0107955 (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.530164.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-117  376.7   0.0   7.4e-117  376.6   0.0    1.0  1  NCBI__GCF_000330705.1:WP_017548940.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017548940.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.6   0.0  7.4e-117  7.4e-117       1     414 [.      11     426 ..      11     427 .. 0.96

  Alignments for each domain:
  == domain 1  score: 376.6 bits;  conditional E-value: 7.4e-117
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lkepea 71 
                                           g +++pg+KSi+hR+l+laaLaeg+t+++ +LkseDt  t+e++r++Ga+++e+++ +++e  g   l+ p  
  NCBI__GCF_000330705.1:WP_017548940.1  11 GTLRVPGDKSITHRSLMLAALAEGRTEIHLPLKSEDTYRTMEIMRAIGADITESGDIWIVESRGHahLHSPAG 83 
                                           6799************************************************99*******99888899999* PP

                             TIGR01356  72 eldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkggi 144
                                            l+ gnsGtt Rl++g+la ++ e +++gd+s+++RP++r+  +L  +ga+i+ k+ e+++P++i  +   +i
  NCBI__GCF_000330705.1:WP_017548940.1  84 PLYTGNSGTTSRLIIGLLAGLGLEAEFSGDDSINRRPMDRVQRPLLDMGADIRLKD-EKYPPVHIYPKPLKAI 155
                                           *****************************************************888.57*******96555** PP

                             TIGR01356 145 velsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykq 217
                                            +  + aS+Q+ksa+lla+   l a+++++v e+  sr++ ei++k+++++   ++ +d+  i+++gg++ ++
  NCBI__GCF_000330705.1:WP_017548940.1 156 DYDMPIASAQVKSAVLLAG---LFAEGTTVVRESSPSRDHSEIMMKQFGAE---LSSKDG-VISLTGGKNLTS 221
                                           *******************...77899****************98887766...999998.999999999888 PP

                             TIGR01356 218 kevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr.......dveveg 282
                                            +v+v+gD+SsAaf+la+a+++++  +t+en+  n+t+ +  i++vLe m a++e+e+         +++   
  NCBI__GCF_000330705.1:WP_017548940.1 222 ADVTVPGDISSAAFPLALAILKPGtSITIENVSLNPTRSG--ILEVLEMMDANIEIETLPgdgeaigNITASY 292
                                           89**********************9***************..889************9888899999999999 PP

                             TIGR01356 283 asklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgll 354
                                           + +l+g+++  + +++liDe+p+la+laa+ +  +++ ++ elR kE+dRi+a+++eL+k+G++ ee+edg++
  NCBI__GCF_000330705.1:WP_017548940.1 293 TPELRGFDIsGEIIPRLIDEIPILALLAAYSNESCTVSDAGELRFKETDRIRAVVDELSKFGIRFEEKEDGFT 365
                                           *********99************************************************************** PP

                             TIGR01356 355 ieGkk.kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           + +++ +   g  v++y+DHRi+m+l + +++ + +++i+d++++++s+P F+++le+l +
  NCBI__GCF_000330705.1:WP_017548940.1 366 VLPGEiEPAAGTAVKGYHDHRIIMMLIIFSIVSDTPLNIDDTSAIDISYPGFINDLESLRK 426
                                           ****9888899**********************************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (428 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: 00:00:00.01
# Mc/sec: 16.66
//
[ok]

This GapMind analysis is from Jul 26 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 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