Alignments for a candidate for aroA in Beijerinckia indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Beijerinckia indica ATCC 9039

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_012384618.1 BIND_RS08260 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A1Z0H6
         (444 letters)



>NCBI__GCF_000019845.1:WP_012384618.1
          Length = 424

 Score =  512 bits (1318), Expect = e-149
 Identities = 260/408 (63%), Positives = 303/408 (74%)

Query: 35  VTPPNFPLTGKVAPPGSKSITNRALLLAALAKGTSRLSGALKSDDTRHMSVALRQMGVTI 94
           ++PP  PL G + PPGSKSITNRALLLAALAKG SRL+GAL SDDT +M+ AL+ MGV I
Sbjct: 13  LSPPGQPLQGHIRPPGSKSITNRALLLAALAKGESRLTGALASDDTAYMAKALKAMGVGI 72

Query: 95  DEPDDTTFVVTSQGSLQLPAQPLFLGNAGTAMRFLTAAVATVQGTVVLDGDEYMQKRPIG 154
           + PD TTF V   G L  P + LFLGNAGTA RFLTAA A   G VV+DGD  M+KRPI 
Sbjct: 73  ESPDATTFHVKGTGHLHAPGETLFLGNAGTATRFLTAAAALADGRVVIDGDANMRKRPIA 132

Query: 155 PLLATLGQNGIQVDSPTGCPPVTVHGMGKVQAKRFEIDGGLSSQYVSALLMLAACGEAPI 214
           PL+  L   G+ +++PTGCPPVT+ G G+V A    ID GLSSQYVSALLMLA CGE PI
Sbjct: 133 PLVTALQSLGVSIEAPTGCPPVTIDGRGRVAAGDVSIDAGLSSQYVSALLMLAPCGEGPI 192

Query: 215 EVALTGKDIGARGYVDLTLDCMRAFGAQVDAVDDTTWRVAPTGYTAHDYLIEPDASAATY 274
            + L G  IGARGYVDLTL  M  FGA+V   D+ +W +APTGY A D++IEPDASAATY
Sbjct: 193 RIVLQGTGIGARGYVDLTLAAMHHFGAEVLQKDEVSWTLAPTGYRARDFVIEPDASAATY 252

Query: 275 LWAAEVLTGGRIDIGVAAQDFTQPDAKAQAVIAQFPNMQATVVGSQMQDAIPTLAVLAAF 334
           LWAA VLT G ID+GV A  FTQPDAKA ++I  FP+M A + GSQ+QDA+PTLAV+AAF
Sbjct: 253 LWAAAVLTQGTIDLGVPASAFTQPDAKAYSLITSFPHMPAVIEGSQIQDAVPTLAVMAAF 312

Query: 335 NNTPVRFTELANLRVKECDRVQALHDGLNEIRPGLATIEGDDLLVASDPALAGTACTALI 394
           N TPVRFT++ANLRVKECDR+ AL   L  I P LA  EGDDL+V  DPAL G    A+I
Sbjct: 313 NKTPVRFTDIANLRVKECDRIHALATELARITPDLAREEGDDLIVTGDPALIGRRTDAII 372

Query: 395 DTHADHRIAMCFALAGLKVSGVRIQDPDCVAKTYPDYWKAWPSLGVHL 442
           +T+ DHRIAM FALAGL + G+ I DPDCVAKTYP +W    SLGV L
Sbjct: 373 ETYDDHRIAMSFALAGLMMDGLTILDPDCVAKTYPGFWNDLGSLGVRL 420


Lambda     K      H
   0.318    0.134    0.400 

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: 620
Number of extensions: 17
Number of successful extensions: 2
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: 444
Length of database: 424
Length adjustment: 32
Effective length of query: 412
Effective length of database: 392
Effective search space:   161504
Effective search space used:   161504
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: 51 (24.3 bits)

Align candidate WP_012384618.1 BIND_RS08260 (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.3565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-109  352.5   0.0   6.8e-107  343.7   0.0    2.0  1  lcl|NCBI__GCF_000019845.1:WP_012384618.1  BIND_RS08260 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012384618.1  BIND_RS08260 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.7   0.0  6.8e-107  6.8e-107       1     413 [.      22     417 ..      22     419 .. 0.93

  Alignments for each domain:
  == domain 1  score: 343.7 bits;  conditional E-value: 6.8e-107
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgglke 68 
                                               g+i+ pgsKSi++RalllaaLa+ge+++t+ L s+Dt ++ +al+++G+ +e  +  +++++g g l+ 
  lcl|NCBI__GCF_000019845.1:WP_012384618.1  22 GHIRPPGSKSITNRALLLAALAKGESRLTGALASDDTAYMAKALKAMGVGIEsPDATTFHVKGTGHLHA 90 
                                               789*************************************************55599*******99*** PP

                                 TIGR01356  69 peaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                               p ++l lgn+Gt++R+lt+++ala+g vv++gd  ++kRPi +lv+aL++lg++ie+ +  g++P++i+
  lcl|NCBI__GCF_000019845.1:WP_012384618.1  91 PGETLFLGNAGTATRFLTAAAALADGRVVIDGDANMRKRPIAPLVTALQSLGVSIEAPT--GCPPVTID 157
                                               ********************************************************977..8******* PP

                                 TIGR01356 138 gp..lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                               g   + +g v +++  SsQy+sall++ap  + +  + ++g+ +  r y+++tL+ +++fg ev ++de
  lcl|NCBI__GCF_000019845.1:WP_012384618.1 158 GRgrVAAGDVSIDAGLSSQYVSALLMLAPCGEGPIRIVLQGTGIGARGYVDLTLAAMHHFGAEVLQKDE 226
                                               *986666************************************************************** PP

                                 TIGR01356 205 rkivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveve 273
                                                ++++ +++ y+ +++ +e DaS+A+++ aaa++t++++ +    ++ tq+d+++ +            
  lcl|NCBI__GCF_000019845.1:WP_012384618.1 227 VSWTLAPTG-YRARDFVIEPDASAATYLWAAAVLTQGTIDLGVPASAFTQPDAKAYS------------ 282
                                               999999987.99999***************************99********43333............ PP

                                 TIGR01356 274 eqrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLekl 342
                                                   +++    ++ +    i+ +++ D++ptlav+aaf +++ r ++i++lRvkE+dRi+a+a+eL+++
  lcl|NCBI__GCF_000019845.1:WP_012384618.1 283 ----LITS-FPHM-PAV--IEGSQIQDAVPTLAVMAAFNKTPVRFTDIANLRVKECDRIHALATELARI 343
                                               ....3333.2334.455..7889999******************************************* PP

                                 TIGR01356 343 Gve.veeledgllieGkk...kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfe 407
                                                 + ++e  d l+++G      +  +a ++tydDHRiam++a++gl ++ +++i d+ cvak++P F++
  lcl|NCBI__GCF_000019845.1:WP_012384618.1 344 TPDlAREEGDDLIVTGDPaliGRRTDAIIETYDDHRIAMSFALAGLMMD-GLTILDPDCVAKTYPGFWN 411
                                               9983578889*******9777777779*********************9.******************* PP

                                 TIGR01356 408 vleqlg 413
                                               +l +lg
  lcl|NCBI__GCF_000019845.1:WP_012384618.1 412 DLGSLG 417
                                               *99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (424 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.86
//
[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