Alignments for a candidate for aroA in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Halorhodospira halophila SL1

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011813374.1 HHAL_RS02875 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000015585.1:WP_011813374.1
          Length = 444

 Score =  454 bits (1168), Expect = e-132
 Identities = 243/439 (55%), Positives = 305/439 (69%), Gaps = 5/439 (1%)

Query: 2   DYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGA 61
           +++  P   L GE  VPGDKSISHRAV+L A+A+G T++ G L GAD LA +   + +G 
Sbjct: 5   NWRVAPGGALHGEARVPGDKSISHRAVMLGALADGTTRITGMLEGADVLATIDVFRALGV 64

Query: 62  SIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQ 121
           +I+  E +  + V GVG  GL+ P   LD GNSGT++RLL+GLLAG PF+TVLTGD+SL 
Sbjct: 65  AIEGPE-QGAVTVHGVGWEGLRPPARELDVGNSGTSMRLLAGLLAGLPFDTVLTGDASLN 123

Query: 122 RRPMKRIIDPLTLMGAKID-STGNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLY 180
           RRPM+R+ +PL  MGA+I  S     PL+I+G   L GI Y LP+ASAQVKS LLLAG+ 
Sbjct: 124 RRPMRRVTEPLAEMGARITTSDAGTAPLRIHGGSPLAGIDYTLPVASAQVKSALLLAGMR 183

Query: 181 ARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFF 240
           A G TC+TEPAP+RDHTER+L+ F Y + +D  ++C+ GG +L    + +P DISSAAF 
Sbjct: 184 AEGHTCVTEPAPTRDHTERMLQGFGYPVSRDLATVCLEGGRRLYGTGVDVPADISSAAFL 243

Query: 241 IVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARL 300
           +VAA+I PGS + L  VG NPTR GV+ +L+ MGADIEV    E   EP AD+ VR A L
Sbjct: 244 LVAASIAPGSDLTLRHVGWNPTRTGVVEILRRMGADIEVLSTDEVGGEPVADLRVRSAAL 303

Query: 301 KGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIA 360
           +GI IP + VPL IDEFP L IAAA A+G+T L  AAELRVKE+DRIA M +GLQ LG+ 
Sbjct: 304 RGIAIPEELVPLAIDEFPALFIAAACAEGETQLTGAAELRVKESDRIAVMAEGLQTLGVT 363

Query: 361 AESLPDGVIIQG-GTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFV 419
            E   DGV I G   L GG V+S+ DHRIAMAFAVA   A+ PV I  C+NV+TSFP FV
Sbjct: 364 VEPREDGVRIVGQPVLGGGRVHSHTDHRIAMAFAVAALRAEAPVEIEACENVRTSFPGFV 423

Query: 420 ELANEVGMNVK--GVRGRG 436
           EL   +GM V+  G   RG
Sbjct: 424 ELLRRLGMGVEVDGPHDRG 442


Lambda     K      H
   0.318    0.137    0.392 

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: 659
Number of extensions: 35
Number of successful extensions: 6
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: 438
Length of database: 444
Length adjustment: 32
Effective length of query: 406
Effective length of database: 412
Effective search space:   167272
Effective search space used:   167272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011813374.1 HHAL_RS02875 (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.25226.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.5e-133  428.9   0.0   1.1e-132  428.7   0.0    1.0  1  lcl|NCBI__GCF_000015585.1:WP_011813374.1  HHAL_RS02875 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015585.1:WP_011813374.1  HHAL_RS02875 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.7   0.0  1.1e-132  1.1e-132       1     414 [.      16     431 ..      16     432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 428.7 bits;  conditional E-value: 1.1e-132
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               ge ++pg+KSishRa++l+aLa+g+t++t++L+++D+lat++++r+lG+ +e  e++ ++++gvg   l
  lcl|NCBI__GCF_000015585.1:WP_011813374.1  16 GEARVPGDKSISHRAVMLGALADGTTRITGMLEGADVLATIDVFRALGVAIEgPEQGAVTVHGVGWegL 84 
                                               7899************************************************777********998889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               + p +eld+gnsGt++Rll g+la +++++vltgd sl++RP++r++e+L e+ga+i  ++ +g++Pl+
  lcl|NCBI__GCF_000015585.1:WP_011813374.1  85 RPPARELDVGNSGTSMRLLAGLLAGLPFDTVLTGDASLNRRPMRRVTEPLAEMGARITTSD-AGTAPLR 152
                                               999*******************************************************877.79***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               i+g++++ gi +  + aS+Q+ksallla+    +a++ + v+e+  +r+++e++L+ ++     v+++ 
  lcl|NCBI__GCF_000015585.1:WP_011813374.1 153 IHGGSPLaGIDYTLPVASAQVKSALLLAG---MRAEGHTCVTEPAPTRDHTERMLQGFGYP---VSRDL 215
                                               ****9988*********************...67899******************998876...99987 PP

                                 TIGR01356 204 erkivvkggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                 ++ ++gg   y++  v+v++D+SsAaf+l+aa i+++ ++t++++g n+t+++  ++++L++mGad+
  lcl|NCBI__GCF_000015585.1:WP_011813374.1 216 A-TVCLEGGRRlYGTG-VDVPADISSAAFLLVAASIAPGsDLTLRHVGWNPTRTG--VVEILRRMGADI 280
                                               6.9******9988888.**********************9***************..888********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               ev +++        d++v+ +  l+g+ + ++ v+ +iDe+p+l ++aa+Aeget++++++elRvkEsd
  lcl|NCBI__GCF_000015585.1:WP_011813374.1 281 EVLSTDevggepvaDLRVR-SAALRGIAIpEELVPLAIDEFPALFIAAACAEGETQLTGAAELRVKESD 348
                                               ***9999************.678******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399
                                               Ria++ae L++lGv+ve++edg+ i G+   l g++v+++ DHRiama+av++l+ae++veie  e v+
  lcl|NCBI__GCF_000015585.1:WP_011813374.1 349 RIAVMAEGLQTLGVTVEPREDGVRIVGQ-PVLGGGRVHSHTDHRIAMAFAVAALRAEAPVEIEACENVR 416
                                               ****************************.6*************************************** PP

                                 TIGR01356 400 ksfPeFfevleqlga 414
                                               +sfP F+e+l++lg+
  lcl|NCBI__GCF_000015585.1:WP_011813374.1 417 TSFPGFVELLRRLGM 431
                                               ***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (444 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: 9.72
//
[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