Alignments for a candidate for aroC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Pedobacter sp. GW460-11-11-14-LB5

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate CA265_RS11645 CA265_RS11645 chorismate synthase

Query= BRENDA::B5AAU3
         (442 letters)



>FitnessBrowser__Pedo557:CA265_RS11645
          Length = 365

 Score =  370 bits (950), Expect = e-107
 Identities = 192/362 (53%), Positives = 245/362 (67%), Gaps = 3/362 (0%)

Query: 54  AGNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKE 113
           AGN FG  F++ T+GESHG  +G +I GCP ++ +  + +Q +LD+R+PGQS+ITT RKE
Sbjct: 2   AGNSFGQLFRITTFGESHGVAIGVIIDGCPAQLDIDMDFIQSELDKRKPGQSKITTQRKE 61

Query: 114 TDTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQ 173
           +DT +ILSG +EG +TGTPI + +PN DQR  DY      YRPSHAD  YD KYG+R  +
Sbjct: 62  SDTVQILSGVFEGKSTGTPIALLIPNEDQRSKDYGHNVDVYRPSHADYVYDAKYGIRDHR 121

Query: 174 GGGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIE 233
           GGGRSSARET  RVAAGA+AK  LK + G+EI A V+ V  +  P    +  +  L   E
Sbjct: 122 GGGRSSARETAARVAAGAIAKLFLKQQ-GIEIFAHVTSVGTIEAPNLESNDLSALLQIRE 180

Query: 234 SNICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAM 293
            NI RC DP  A +MI+ ID VR +G+++GG + C+ +  P GLG PVFDKL A L KAM
Sbjct: 181 ENIVRCADPATAHEMIEFIDSVRKDGDTVGGKIGCVVKGCPAGLGEPVFDKLHADLGKAM 240

Query: 294 LSLPASKGFEIGSGFAGTDLTGSEHND--EFYMDEGGNVRTRTNRSGGVQGGISNGETIY 351
           LS+ A  GFE GSGFAG++L GS+HND  +    +    +T TN +GG+ GGISNG  I 
Sbjct: 241 LSINAVHGFEYGSGFAGSELRGSQHNDIPQPKAADSKVFKTTTNYAGGILGGISNGMDIT 300

Query: 352 FKVAFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMDQLMAH 411
           FKVAFKP ATI   Q T+    E  E+  +GRHDPCVVPRAV +VE MAALVL DQ + +
Sbjct: 301 FKVAFKPVATIMHNQQTINAAGEASEIKGKGRHDPCVVPRAVVIVEAMAALVLADQFLRN 360

Query: 412 VA 413
            A
Sbjct: 361 KA 362


Lambda     K      H
   0.317    0.135    0.396 

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: 436
Number of extensions: 23
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: 442
Length of database: 365
Length adjustment: 31
Effective length of query: 411
Effective length of database: 334
Effective search space:   137274
Effective search space used:   137274
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate CA265_RS11645 CA265_RS11645 (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.25922.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-141  457.2   1.2   1.9e-141  457.1   1.2    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS11645  CA265_RS11645 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS11645  CA265_RS11645 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.1   1.2  1.9e-141  1.9e-141       1     349 [.      10     362 ..      10     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 457.1 bits;  conditional E-value: 1.9e-141
                                  TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTt 68 
                                                +r+ttfGeSHg a+g+iidG+Pa l ++++ iq+el++R+pgqs+ t++rkE+D+v+ilsGvfeGk t
  lcl|FitnessBrowser__Pedo557:CA265_RS11645  10 FRITTFGESHGVAIGVIIDGCPAQLDIDMDFIQSELDKRKPGQSKITTQRKESDTVQILSGVFEGKST 77 
                                                89****************************************************************** PP

                                  TIGR00033  69 GaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklL 136
                                                G+Pialli N+d+rskdy +  +++RP+Hady+y  KYgi+d++gggrsSaReTaarvaaGa+ak +L
  lcl|FitnessBrowser__Pedo557:CA265_RS11645  78 GTPIALLIPNEDQRSKDYGHNVDVYRPSHADYVYDAKYGIRDHRGGGRSSARETAARVAAGAIAKLFL 145
                                                ******************************************************************** PP

                                  TIGR00033 137 ketagieivayvvklgeveleeesak..eiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgv 202
                                                k+ +giei a+v+++g +e+++ + +  +   +  +++ vrc+d+ +++em e id+++kdgd+vGg+
  lcl|FitnessBrowser__Pedo557:CA265_RS11645 146 KQ-QGIEIFAHVTSVGTIEAPNLESNdlSALLQIREENIVRCADPATAHEMIEFIDSVRKDGDTVGGK 212
                                                **.99***************98777756556778888******************************* PP

                                  TIGR00033 203 vevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle...ddkir 267
                                                + +vv++ p+glGep+fdkl+a l++a+lsinAv g+e G+GF+  + rGs++nD  + +   ++ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS11645 213 IGCVVKGCPAGLGEPVFDKLHADLGKAMLSINAVHGFEYGSGFAGSELRGSQHNDIPQPKaadSKVFK 280
                                                *******************************************************4433222367789 PP

                                  TIGR00033 268 rktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEam 335
                                                + tn  GGi+GGi+nG+di++++a+Kp++ti ++++t++ +++ +    kgRhDpcvvprav++vEam
  lcl|FitnessBrowser__Pedo557:CA265_RS11645 281 TTTNYAGGILGGISNGMDITFKVAFKPVATIMHNQQTINAAGEASEIKGKGRHDPCVVPRAVVIVEAM 348
                                                999************************************9766555555******************* PP

                                  TIGR00033 336 valvladallekra 349
                                                 alvlad++l+++a
  lcl|FitnessBrowser__Pedo557:CA265_RS11645 349 AALVLADQFLRNKA 362
                                                **********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (365 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: 7.57
//
[ok]

This GapMind analysis is from Apr 09 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