Alignments for a candidate for aroC in Hippea alviniae EP5-r

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Hippea alviniae EP5-r

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_022670212.1 G415_RS0103530 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000420385.1:WP_022670212.1
          Length = 383

 Score =  377 bits (969), Expect = e-109
 Identities = 202/390 (51%), Positives = 271/390 (69%), Gaps = 11/390 (2%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           +RFL AGESHGK L AI+EG+PA L +  + IN +L  RQ GYGRGGR KIEKD  E LS
Sbjct: 2   IRFLDAGESHGKALIAIIEGLPAGLKIDSDFINRQLLLRQSGYGRGGRQKIEKDRVEFLS 61

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           GVRFG+T+GSPIA+ I+NRD+ENW++ M    E S       RPRPGHADL+G +KY++ 
Sbjct: 62  GVRFGETIGSPIAILIKNRDFENWRDIMEPFAEKSRQ-RRVNRPRPGHADLTGYLKYDRD 120

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEVEELKDKSYFANPE 185
           D+R+ILER+SARETA RVAVG++C+  L E G++I SFV SIG+ + E          PE
Sbjct: 121 DIRDILERSSARETAIRVAVGSICELLLKELGVRIISFVRSIGKIKTE--------IKPE 172

Query: 186 KLLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGSHIQW 245
               +  K  DS +  P  + ++     I+E K++G++LGGV EV A  V  G+GS++QW
Sbjct: 173 VNDEFERKIIDSLVFCPDKKVEDLMIAEIEEAKKEGDTLGGVVEVVASGVVAGVGSYVQW 232

Query: 246 DRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHSNNLGGTE 305
           DRR+D R++ ++MSIQA+K VEIG GFE A +FGSQVHDEI +    GY R SN  GG E
Sbjct: 233 DRRLDARVSFSLMSIQAVKAVEIGDGFENAYKFGSQVHDEIVYD--SGYKRVSNRAGGIE 290

Query: 306 GGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASVVGEAMLA 365
           GG++NG  IVVR  MKPIPTL+  L+SV+I+T EE  +  ER+D+ AVP+ S+V  +++A
Sbjct: 291 GGMSNGEDIVVRAYMKPIPTLRKGLKSVNIDTHEEDISAFERSDVTAVPSLSIVARSVVA 350

Query: 366 IVLADALLEKLGGDFMEEVKKRFEDYVNHV 395
             LA+   EK GGD ++E+K+R E Y  ++
Sbjct: 351 FELANLYAEKFGGDTLKELKERVEAYKKYL 380


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: 453
Number of extensions: 22
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: 398
Length of database: 383
Length adjustment: 31
Effective length of query: 367
Effective length of database: 352
Effective search space:   129184
Effective search space used:   129184
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_022670212.1 G415_RS0103530 (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.1821386.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-122  392.2   0.2   1.1e-121  392.0   0.2    1.0  1  NCBI__GCF_000420385.1:WP_022670212.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022670212.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.0   0.2  1.1e-121  1.1e-121       2     349 ..       3     362 ..       2     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 392.0 bits;  conditional E-value: 1.1e-121
                             TIGR00033   2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPial 74 
                                           r++ +GeSHgkal aii+GlPagl+++ + i+++l  R+ g++r+ r++ E+D+ve+lsGv+ G+T G+Pia+
  NCBI__GCF_000420385.1:WP_022670212.1   3 RFLDAGESHGKALIAIIEGLPAGLKIDSDFINRQLLLRQSGYGRGGRQKIEKDRVEFLSGVRFGETIGSPIAI 75 
                                           78899******************************************************************** PP

                             TIGR00033  75 likNkd..........vrskdyedikelpRPgHadytylkKYgikd.regggrsSaReTaarvaaGavakklL 136
                                           likN+d           + k  +   ++pRPgHad+t+  KY  +d r +++rsSaReTa rva+G++ + lL
  NCBI__GCF_000420385.1:WP_022670212.1  76 LIKNRDfenwrdimepFAEKSRQRRVNRPRPGHADLTGYLKYDRDDiRDILERSSARETAIRVAVGSICELLL 148
                                           ******8888877555445555558899********************************************* PP

                             TIGR00033 137 ketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvs 208
                                           ke  g++i+++v+++g++++e +    ++ ++++ +s v+cpd++ e+ m +ei++akk+gd++Ggvvevv+s
  NCBI__GCF_000420385.1:WP_022670212.1 149 KE-LGVRIISFVRSIGKIKTEIKPEVnDEFERKIIDSLVFCPDKKVEDLMIAEIEEAKKEGDTLGGVVEVVAS 220
                                           **.88************9888655445567888888************************************* PP

                             TIGR00033 209 nvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGG 279
                                           +v +g+G  ++++++lda+++  l+si+AvK+veiGdGFe+a+  Gs+++De+v++  +++r++n+ GGieGG
  NCBI__GCF_000420385.1:WP_022670212.1 221 GVVAGVGsyVQWDRRLDARVSFSLMSIQAVKAVEIGDGFENAYKFGSQVHDEIVYD-SGYKRVSNRAGGIEGG 292
                                           *******999*******************************************985.689************* PP

                             TIGR00033 280 itnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekra 349
                                           ++nGedi+vr+ +Kpipt++k lk+v+++t+e+   + +R+D+++vp  ++v+ ++va+ la++++ek++
  NCBI__GCF_000420385.1:WP_022670212.1 293 MSNGEDIVVRAYMKPIPTLRKGLKSVNIDTHEEDISAFERSDVTAVPSLSIVARSVVAFELANLYAEKFG 362
                                           *****************************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (383 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 18.67
//
[ok]

This GapMind analysis is from Jul 25 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 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