Alignments for a candidate for aroC in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Chlorobium limicola DSM 245

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012465839.1 CLIM_RS04435 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000020465.1:WP_012465839.1
          Length = 397

 Score =  379 bits (972), Expect = e-109
 Identities = 201/397 (50%), Positives = 270/397 (68%), Gaps = 14/397 (3%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           +R+LT+GESHG  LTAI++G+PA + +++ +I+ +L RRQ+GYGRGGRM IE D AE++S
Sbjct: 2   IRYLTSGESHGPALTAIVDGLPAGIDITQNDIDSQLLRRQQGYGRGGRMTIESDKAEVMS 61

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           G+RFGK++GSPI L IRNRDWENW   MA   EP   +   + PRPGHADL+G IKY   
Sbjct: 62  GIRFGKSIGSPITLLIRNRDWENWTTTMARFEEPVEEIAKISIPRPGHADLAGRIKYGFN 121

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIG-------QKEVEELKDK 178
           D+R ++ER+SARETAARVA G++ + FL   GI+IGS+V +IG          VEEL   
Sbjct: 122 DIRPVIERSSARETAARVAAGSLSRVFLKALGIEIGSYVSAIGSAAEPTVNPAVEEL--- 178

Query: 179 SYFANPEKLLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPG 238
               N  + L+   +A+ S +R+     +      IDEVK++G++LGG+ E+F   VP G
Sbjct: 179 --LVNGAECLAL--EADRSSVRMLNKSAEAGAIAAIDEVKKQGDTLGGIIEIFITGVPMG 234

Query: 239 LGSHIQWDRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHS 298
           LGS++Q DRR+D  +  A+MSIQAIKG EIG  FE +R+ GSQVHDE   SE  G  R +
Sbjct: 235 LGSYVQHDRRLDAMLVSALMSIQAIKGAEIGHAFENSRKPGSQVHDEFFLSENTGLERKT 294

Query: 299 NNLGGTEGGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASV 358
           N  GG EG +++G  I +R AMKPI +L  PL S D+ET +   +  ER+D  AVPAA V
Sbjct: 295 NRAGGLEGSMSSGQTIHLRAAMKPISSLVTPLHSFDLETMKPTLSRFERSDTCAVPAAGV 354

Query: 359 VGEAMLAIVLADALLEKLGGDFMEEVKKRFEDYVNHV 395
           V EA++A V+A+ALLEKLGGD   E+K R E Y +H+
Sbjct: 355 VAEAVVAPVIANALLEKLGGDHFIEIKSRLETYRDHL 391


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: 422
Number of extensions: 21
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: 397
Length adjustment: 31
Effective length of query: 367
Effective length of database: 366
Effective search space:   134322
Effective search space used:   134322
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_012465839.1 CLIM_RS04435 (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.29262.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-117  378.3   0.2     2e-117  378.0   0.2    1.0  1  lcl|NCBI__GCF_000020465.1:WP_012465839.1  CLIM_RS04435 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012465839.1  CLIM_RS04435 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.0   0.2    2e-117    2e-117       2     349 ..       3     373 ..       2     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: 378.0 bits;  conditional E-value: 2e-117
                                 TIGR00033   2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 
                                               r++t GeSHg+al+ai+dGlPag+ +t++di ++l rR++g++r+ rm  E+D+ e++sG++ Gk  G+
  lcl|NCBI__GCF_000020465.1:WP_012465839.1   3 RYLTSGESHGPALTAIVDGLPAGIDITQNDIDSQLLRRQQGYGRGGRMTIESDKAEVMSGIRFGKSIGS 71 
                                               899****************************************************************** PP

                                 TIGR00033  71 PiallikNkd.........vrskdyed..ikelpRPgHadytylkKYgikd.regggrsSaReTaarva 127
                                               Pi+lli+N+d            +++e+  + ++pRPgHad++++ KYg++d r  ++rsSaReTaarva
  lcl|NCBI__GCF_000020465.1:WP_012465839.1  72 PITLLIRNRDwenwtttmaRFEEPVEEiaKISIPRPGHADLAGRIKYGFNDiRPVIERSSARETAARVA 140
                                               **********99999876545677777555679************************************ PP

                                 TIGR00033 128 aGavakklLketagieivayvvklgeveleeesak.........eiskerldkspvrcpdaeaekemee 187
                                               aG++ + +Lk   giei +yv+ +g+ + ++ +           e    ++d+s vr+++++ae+   +
  lcl|NCBI__GCF_000020465.1:WP_012465839.1 141 AGSLSRVFLKA-LGIEIGSYVSAIGSAAEPTVNPAveellvngaECLALEADRSSVRMLNKSAEAGAIA 208
                                               ***********.88************766666555577888888788889999**************** PP

                                 TIGR00033 188 eidkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGse 254
                                                id++kk+gd++Gg++e+ +++vp glG  ++ +++lda+l sal+si+A+Kg eiG+ Fe+ + +Gs+
  lcl|NCBI__GCF_000020465.1:WP_012465839.1 209 AIDEVKKQGDTLGGIIEIFITGVPMGLGsyVQHDRRLDAMLVSALMSIQAIKGAEIGHAFENSRKPGSQ 277
                                               ****************************99999************************************ PP

                                 TIGR00033 255 anDelvle.ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDp 322
                                               ++De+ l+ +++++rktn+ GG+eG ++ G+ i++r+a+Kpi+++ +pl++ dlet++++    +R+D 
  lcl|NCBI__GCF_000020465.1:WP_012465839.1 278 VHDEFFLSeNTGLERKTNRAGGLEGSMSSGQTIHLRAAMKPISSLVTPLHSFDLETMKPTLSRFERSDT 346
                                               *****999799********************************************************** PP

                                 TIGR00033 323 cvvpravpvvEamvalvladallekra 349
                                               c+vp+a++v+Ea+va v+a+allek +
  lcl|NCBI__GCF_000020465.1:WP_012465839.1 347 CAVPAAGVVAEAVVAPVIANALLEKLG 373
                                               ***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (397 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: 7.16
//
[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