Alignments for a candidate for aroC in Azospirillum lipoferum B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Azospirillum lipoferum B510

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012974787.1 AZL_RS11825 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000010725.1:WP_012974787.1
          Length = 359

 Score =  435 bits (1118), Expect = e-126
 Identities = 220/361 (60%), Positives = 275/361 (76%), Gaps = 10/361 (2%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLT-EADLQHDLDRRRPGTSRYTTQR 59
           MAGN+ G LFR TT+GESHG A+G +VDG P  + L  E D+Q  +D+RRPG SRYTTQR
Sbjct: 1   MAGNSFGTLFRFTTWGESHGPAIGVVVDGCPSLLDLVAETDIQPWMDKRRPGQSRYTTQR 60

Query: 60  REPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRD 119
           +EPDQV+ILSGVFEG TTGT I LLIENTDQRS+DYS I   FRPGHADYTY QKYG+RD
Sbjct: 61  QEPDQVRILSGVFEGKTTGTPISLLIENTDQRSKDYSDIAGKFRPGHADYTYWQKYGIRD 120

Query: 120 YRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQVEQNP 177
           YRGGGRSSARETA RVAAGA+A+K L     I++RG L Q+G   +D    DW++++ NP
Sbjct: 121 YRGGGRSSARETACRVAAGAVARKVLGS--AIQVRGALVQVGPHRIDHSRWDWAEIDNNP 178

Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237
           FFCPDP       + +  ++K G S GA V +VASGVP GLG+P++D+LD+D+A A+M+I
Sbjct: 179 FFCPDPVAAAQWADYLDGIRKSGSSAGAVVELVASGVPVGLGDPLYDKLDSDLARAMMTI 238

Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEIT--KDG---FQSNHAGGILGGISSGQQIIAHMAL 292
           NAVKGVEIG+GF   AL G +N D++   +DG   F SNHAGGILGGIS+GQ I+   A+
Sbjct: 239 NAVKGVEIGNGFAAAALTGEENADQMRMGQDGRPQFLSNHAGGILGGISTGQDIVVRFAV 298

Query: 293 KPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNA 352
           KPTSSI  P +T++  G + +++TKGRHDPCVGIRAVP+ EAM+A VL DHLLR+RA+  
Sbjct: 299 KPTSSILTPRQTVDTAGNDTDILTKGRHDPCVGIRAVPVGEAMMACVLADHLLRRRAERR 358

Query: 353 D 353
           +
Sbjct: 359 E 359


Lambda     K      H
   0.319    0.138    0.404 

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: 440
Number of extensions: 18
Number of successful extensions: 5
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: 361
Length of database: 359
Length adjustment: 29
Effective length of query: 332
Effective length of database: 330
Effective search space:   109560
Effective search space used:   109560
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: 49 (23.5 bits)

Align candidate WP_012974787.1 AZL_RS11825 (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.26724.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-139  450.5   0.0   2.1e-139  450.3   0.0    1.0  1  lcl|NCBI__GCF_000010725.1:WP_012974787.1  AZL_RS11825 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010725.1:WP_012974787.1  AZL_RS11825 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.3   0.0  2.1e-139  2.1e-139       1     350 [.      10     356 ..      10     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 450.3 bits;  conditional E-value: 2.1e-139
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglel.teediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTt 68 
                                               +r+tt+GeSHg+a+g+++dG+P+ l l  e diq+ +++Rrpgqsr+t++r+E D+v+ilsGvfeGkTt
  lcl|NCBI__GCF_000010725.1:WP_012974787.1  10 FRFTTWGESHGPAIGVVVDGCPSLLDLvAETDIQPWMDKRRPGQSRYTTQRQEPDQVRILSGVFEGKTT 78 
                                               89***********************9725679************************************* PP

                                 TIGR00033  69 GaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLk 137
                                               G+Pi+lli+N+d+rskdy+di+ ++RPgHadyty++KYgi+d++gggrsSaReTa+rvaaGava+k L 
  lcl|NCBI__GCF_000010725.1:WP_012974787.1  79 GTPISLLIENTDQRSKDYSDIAGKFRPGHADYTYWQKYGIRDYRGGGRSSARETACRVAAGAVARKVLG 147
                                               ********************************************************************9 PP

                                 TIGR00033 138 etagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevv 206
                                               +   i++ + +v++g  +++++  +     ++d++p++cpd+ a+++  +++d ++k+g s G+vve+v
  lcl|NCBI__GCF_000010725.1:WP_012974787.1 148 S--AIQVRGALVQVGPHRIDHSRWD---WAEIDNNPFFCPDPVAAAQWADYLDGIRKSGSSAGAVVELV 211
                                               9..69***************98888...479************************************** PP

                                 TIGR00033 207 vsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsG 274
                                               +s+vpvglG+pl+dkld+ la+a+++inAvKgveiG+GF+aa  +G e  D++ +  d++ ++ +n+ G
  lcl|NCBI__GCF_000010725.1:WP_012974787.1 212 ASGVPVGLGDPLYDKLDSDLARAMMTINAVKGVEIGNGFAAAALTGEENADQMRMGqDGRPQFLSNHAG 280
                                               ******************************************************9989999******** PP

                                 TIGR00033 275 GieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvlada 343
                                               Gi+GGi++G+di+vr avKp+++i +p++tvd++++++   tkgRhDpcv +ravpv Eam+a vlad+
  lcl|NCBI__GCF_000010725.1:WP_012974787.1 281 GILGGISTGQDIVVRFAVKPTSSILTPRQTVDTAGNDTDILTKGRHDPCVGIRAVPVGEAMMACVLADH 349
                                               ********************************************************************* PP

                                 TIGR00033 344 llekras 350
                                               ll++ra+
  lcl|NCBI__GCF_000010725.1:WP_012974787.1 350 LLRRRAE 356
                                               **99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (359 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.96
//
[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