Alignments for a candidate for aroC in Sulfurihydrogenibium azorense Az-Fu1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Sulfurihydrogenibium azorense Az-Fu1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012673988.1 SULAZ_RS05650 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000021545.1:WP_012673988.1
          Length = 390

 Score =  487 bits (1253), Expect = e-142
 Identities = 254/397 (63%), Positives = 304/397 (76%), Gaps = 12/397 (3%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           LRFL AGESHG  LTAI+EG P+N+ +S + INHEL RRQ+GYGRGGRMKIEKDT EILS
Sbjct: 2   LRFLNAGESHGPALTAIVEGYPSNVNVSSDRINHELARRQKGYGRGGRMKIEKDTVEILS 61

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           GVRFG TLG+PI L I+N+DWENW + MA+EG+P         PRPGHADL GGIKY   
Sbjct: 62  GVRFGITLGTPITLMIKNKDWENWTDIMAVEGQPIDKR-QILEPRPGHADLIGGIKYGFY 120

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEV--EELKDKSYFAN 183
           DLRN+LERASARET  RVAVGA+CK  L + GIKIGS+V+SIG+K++  EE+K+ SY   
Sbjct: 121 DLRNVLERASARETTTRVAVGALCKILLEDIGIKIGSYVLSIGEKKIYKEEIKNLSYEER 180

Query: 184 PEKLLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGSHI 243
                   E AE+SE+RIP   KDEEFK YID++KE+GESLGGVFEV+ALNVP GLGS+ 
Sbjct: 181 -------FENAENSEVRIPVLGKDEEFKEYIDKMKEEGESLGGVFEVYALNVPIGLGSYS 233

Query: 244 QWDRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHSNNLGG 303
           QWDRR+DG IAQA+MSIQAIKGVEIG GF      G   HDEI WS+ +G++R +N  GG
Sbjct: 234 QWDRRLDGIIAQAIMSIQAIKGVEIGEGFNLTYTTGYNAHDEIFWSKEEGFYRKTNRAGG 293

Query: 304 TEGGITNGMPIVVRVAMKPIPTL--KNPLRSVDIETKEEMKAGKERTDIVAVPAASVVGE 361
            EGG+TNGMPIVVR AMKPIPTL  +  L+SV+++TKE   A KER+DI AVPAA+VV E
Sbjct: 294 LEGGMTNGMPIVVRAAMKPIPTLMRQKSLKSVNVKTKEPFDAAKERSDITAVPAAAVVAE 353

Query: 362 AMLAIVLADALLEKLGGDFMEEVKKRFEDYVNHVKSF 398
           +MLA VLA  +L+K G D   E+KKR EDY  +VKS+
Sbjct: 354 SMLAFVLAREILQKFGKDNWIEIKKRIEDYREYVKSY 390


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: 545
Number of extensions: 17
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: 390
Length adjustment: 31
Effective length of query: 367
Effective length of database: 359
Effective search space:   131753
Effective search space used:   131753
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_012673988.1 SULAZ_RS05650 (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.2347.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-127  410.5   0.1     3e-127  410.3   0.1    1.0  1  lcl|NCBI__GCF_000021545.1:WP_012673988.1  SULAZ_RS05650 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021545.1:WP_012673988.1  SULAZ_RS05650 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.3   0.1    3e-127    3e-127       1     350 [.       2     370 ..       2     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 410.3 bits;  conditional E-value: 3e-127
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++ +GeSHg+al+ai++G P++++++ + i++el+rR++g++r+ rm+ E+D+veilsGv+ G T G
  lcl|NCBI__GCF_000021545.1:WP_012673988.1   2 LRFLNAGESHGPALTAIVEGYPSNVNVSSDRINHELARRQKGYGRGGRMKIEKDTVEILSGVRFGITLG 70 
                                               68999**************************************************************** PP

                                 TIGR00033  70 aPiallikNkd.........vrskdyed.ikelpRPgHadytylkKYgikd.regggrsSaReTaarva 127
                                               +Pi+l+ikNkd         v+++++++     pRPgHad+ +  KYg++d r+ ++r+SaReT++rva
  lcl|NCBI__GCF_000021545.1:WP_012673988.1  71 TPITLMIKNKDwenwtdimaVEGQPIDKrQILEPRPGHADLIGGIKYGFYDlRNVLERASARETTTRVA 139
                                               ******************999999999945568************************************ PP

                                 TIGR00033 128 aGavakklLketagieivayvvklgeveleeesak....eiskerldkspvrcpdaeaekemeeeidka 192
                                               +Ga+ k lL++  gi+i +yv ++ge+++ +e++k    e+  e++++s+vr+p   +++e +e+idk+
  lcl|NCBI__GCF_000021545.1:WP_012673988.1 140 VGALCKILLED-IGIKIGSYVLSIGEKKIYKEEIKnlsyEERFENAENSEVRIPVLGKDEEFKEYIDKM 207
                                               **********9.88**************99999997766556667777********************* PP

                                 TIGR00033 193 kkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDel 259
                                               k++g+s+Ggv ev + nvp glG  ++++++ld+ +a+a++si+A+KgveiG+GF++++++G +a+De+
  lcl|NCBI__GCF_000021545.1:WP_012673988.1 208 KEEGESLGGVFEVYALNVPIGLGsySQWDRRLDGIIAQAIMSIQAIKGVEIGEGFNLTYTTGYNAHDEI 276
                                               ***********************999******************************************* PP

                                 TIGR00033 260 vle.ddkirrktnnsGGieGGitnGedirvriavKpiptik..kplktvdletkekakatkgRhDpcvv 325
                                                ++ ++++ rktn+ GG+eGG+tnG++i+vr+a+Kpipt+   k lk+v+++tke+  a+k+R+D ++v
  lcl|NCBI__GCF_000021545.1:WP_012673988.1 277 FWSkEEGFYRKTNRAGGLEGGMTNGMPIVVRAAMKPIPTLMrqKSLKSVNVKTKEPFDAAKERSDITAV 345
                                               **9999*********************************96225689********************** PP

                                 TIGR00033 326 pravpvvEamvalvladallekras 350
                                               p+a++v+E+m+a+vla ++l+k+++
  lcl|NCBI__GCF_000021545.1:WP_012673988.1 346 PAAAVVAESMLAFVLAREILQKFGK 370
                                               *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (390 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: 8.93
//
[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