Alignments for a candidate for aroC in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Thermocrinis albus DSM 14484

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012991136.1 THAL_RS00450 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000025605.1:WP_012991136.1
          Length = 387

 Score =  586 bits (1511), Expect = e-172
 Identities = 296/393 (75%), Positives = 328/393 (83%), Gaps = 8/393 (2%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           +RFLTAGESHG+ L  ILEGIPANL LS E+IN +LRRRQ+GYGRGGRMKIE+D  EILS
Sbjct: 3   IRFLTAGESHGQALVCILEGIPANLELSAEDINRDLRRRQKGYGRGGRMKIEQDQVEILS 62

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           GVRFGKT G+PIAL I+NRDWENWKEKMA+EGE   S VPFTRPRPGHADL+GGIKYNQR
Sbjct: 63  GVRFGKTTGAPIALLIKNRDWENWKEKMAVEGERPSSAVPFTRPRPGHADLAGGIKYNQR 122

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEVEELKDKSYFANPE 185
           DLRNILERASARETA R AVGAVCKKFL E GIK+GS+VVSIG                E
Sbjct: 123 DLRNILERASARETACRCAVGAVCKKFLQELGIKVGSYVVSIGSLSPP--------IQEE 174

Query: 186 KLLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGSHIQW 245
            L   H  AE+S +R P P KD  F   IDE K+ GESLGGVFEVFALNVPPGLGSH QW
Sbjct: 175 DLEKRHLLAEESVVRFPDPTKDPLFMELIDEAKQMGESLGGVFEVFALNVPPGLGSHTQW 234

Query: 246 DRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHSNNLGGTE 305
           DRRIDGRIAQAMMSIQAIKGVEIGLGFEAA+R GSQVHDEIGW   +G+FR++N+LGGTE
Sbjct: 235 DRRIDGRIAQAMMSIQAIKGVEIGLGFEAAKRKGSQVHDEIGWDPERGFFRYTNHLGGTE 294

Query: 306 GGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASVVGEAMLA 365
           GG+TNGMPI+VR AMKPIPTL  PLRSVDI+TKEE+ AGKERTD+VAVPAASVVGEAMLA
Sbjct: 295 GGVTNGMPILVRCAMKPIPTLARPLRSVDIQTKEEVSAGKERTDVVAVPAASVVGEAMLA 354

Query: 366 IVLADALLEKLGGDFMEEVKKRFEDYVNHVKSF 398
            V+A ALLEKLGGDFMEE+K+R+  Y+ +VKSF
Sbjct: 355 FVVAQALLEKLGGDFMEEIKERYARYLEYVKSF 387


Lambda     K      H
   0.317    0.137    0.394 

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: 581
Number of extensions: 13
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: 398
Length of database: 387
Length adjustment: 31
Effective length of query: 367
Effective length of database: 356
Effective search space:   130652
Effective search space used:   130652
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: 50 (23.9 bits)

Align candidate WP_012991136.1 THAL_RS00450 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

# 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/TIGR00033.hmm
# target sequence database:        /tmp/gapView.8252.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00033  [M=351]
Accession:   TIGR00033
Description: aroC: chorismate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-131  425.0   0.0   1.2e-131  424.8   0.0    1.0  1  lcl|NCBI__GCF_000025605.1:WP_012991136.1  THAL_RS00450 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025605.1:WP_012991136.1  THAL_RS00450 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.8   0.0  1.2e-131  1.2e-131       2     349 ..       4     366 ..       3     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: 424.8 bits;  conditional E-value: 1.2e-131
                                 TIGR00033   2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 
                                               r++t+GeSHg+al++i++G+Pa+lel++edi+++l+rR++g++r+ rm+ E+D+veilsGv+ GkTtGa
  lcl|NCBI__GCF_000025605.1:WP_012991136.1   4 RFLTAGESHGQALVCILEGIPANLELSAEDINRDLRRRQKGYGRGGRMKIEQDQVEILSGVRFGKTTGA 72 
                                               89******************************************************************* PP

                                 TIGR00033  71 PiallikNkd.........vrskdyed.......ikelpRPgHadytylkKYgikd.regggrsSaReT 122
                                               PiallikN+d         v+               ++pRPgHad+++  KY+ +d r++++r+SaReT
  lcl|NCBI__GCF_000025605.1:WP_012991136.1  73 PIALLIKNRDwenwkekmaVE-----GerpssavPFTRPRPGHADLAGGIKYNQRDlRNILERASARET 136
                                               **********87776664433.....144455667899******************************* PP

                                 TIGR00033 123 aarvaaGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeeeid 190
                                               a+r a+Gav kk+L+e  gi++ +yvv++g+++ + ++ + e  +  +++s vr+pd++++    e+id
  lcl|NCBI__GCF_000025605.1:WP_012991136.1 137 ACRCAVGAVCKKFLQE-LGIKVGSYVVSIGSLSPPIQEEDlEKRHLLAEESVVRFPDPTKDPLFMELID 204
                                               ****************.88************99997777744344556679****************** PP

                                 TIGR00033 191 kakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanD 257
                                               +ak+ g+s+Ggv ev + nvp glG   ++++++d+++a+a++si+A+KgveiG GFeaa+++Gs+++D
  lcl|NCBI__GCF_000025605.1:WP_012991136.1 205 EAKQMGESLGGVFEVFALNVPPGLGshTQWDRRIDGRIAQAMMSIQAIKGVEIGLGFEAAKRKGSQVHD 273
                                               *************************9889**************************************** PP

                                 TIGR00033 258 elvle.ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvv 325
                                               e+ ++ + ++ r tn++GG+eGG+tnG++i vr a+Kpipt+++pl++vd++tke+++a k+R D+++v
  lcl|NCBI__GCF_000025605.1:WP_012991136.1 274 EIGWDpERGFFRYTNHLGGTEGGVTNGMPILVRCAMKPIPTLARPLRSVDIQTKEEVSAGKERTDVVAV 342
                                               *****999999********************************************************** PP

                                 TIGR00033 326 pravpvvEamvalvladallekra 349
                                               p+a++v Eam+a+v+a+allek +
  lcl|NCBI__GCF_000025605.1:WP_012991136.1 343 PAASVVGEAMLAFVVAQALLEKLG 366
                                               ********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (387 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.97
//
[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