Alignments for a candidate for aroA in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Bacteroides thetaiotaomicron VPI-5482

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate 351714 BT2186 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file)

Query= uniprot:I9A2E3
         (408 letters)



>FitnessBrowser__Btheta:351714
          Length = 410

 Score =  559 bits (1441), Expect = e-164
 Identities = 286/403 (70%), Positives = 326/403 (80%)

Query: 1   MQIKVTAPAQIHTTIQLPSSKSISNRALIINALGNRTFQLENLSDCDDTQVMIHALNDGK 60
           M  K+ +P+ +  TIQLP+SKSISNRALIINALG   +  ENLSDCDDTQVMI AL +GK
Sbjct: 2   MLYKLISPSMVKATIQLPASKSISNRALIINALGKGIYPPENLSDCDDTQVMIKALTEGK 61

Query: 61  NTIDIMAAGTAMRFLTAYLSVTPGTRIITGTQRMQQRPIQVLVNALRELGAEIEYIINDG 120
            TIDIMAAGTAMRFLTAYLS T G RIITGT RMQQRPIQ+LVNALRELGAEIEY  N+G
Sbjct: 62  ETIDIMAAGTAMRFLTAYLSATSGERIITGTARMQQRPIQILVNALRELGAEIEYTHNEG 121

Query: 121 YPPLRITGHKLQKDTISLPGNVSSQYISALLMIAPILSNGLTLTLTGEIISRPYINLTLQ 180
           YPPLRI G +L+ + I+L GNVSSQYISALLMI P+L +GLTL LTGEIISRPYINLTLQ
Sbjct: 122 YPPLRIKGAELKGNEITLKGNVSSQYISALLMIGPVLKDGLTLHLTGEIISRPYINLTLQ 181

Query: 181 LMNDFGARAKWLNEYQLKVEPQPYQSIPFYVESDWSAASYWYQIAALSNKAEIILPGLFE 240
           LM DFGA+A W +   + V PQPYQS+PF VESDWSAASYWYQIAALS +AEI L GLF 
Sbjct: 182 LMQDFGAKAAWTSPSSISVAPQPYQSVPFTVESDWSAASYWYQIAALSPEAEIELLGLFR 241

Query: 241 TSYQGDSKVAEIFQLLGIESIYGNKTVTLKKTDKITERLDYDFINQPDLAQTFVVTCALM 300
            SYQGDS+ AE+F  LGI + +  K V +KKT K  ERL+ DF++ PDLAQTFVVTCAL+
Sbjct: 242 NSYQGDSRGAEVFSRLGITTEFTPKGVKIKKTGKTPERLEEDFVDIPDLAQTFVVTCALL 301

Query: 301 NIPFRFSGLQSLKIKETDRMAALIQEMGKLGYILHETDDRILSWEGERCEMTADVAIDTY 360
           NIPFRF+GLQSLKIKETDR+AAL  E+ KLGY++ E +D +L W GERCE  A   I TY
Sbjct: 302 NIPFRFTGLQSLKIKETDRIAALRTELKKLGYLIEEENDSVLMWNGERCEPEAVPVIATY 361

Query: 361 EDHRMAMAFAPACVVMPEIRINNPQVVSKSYPYYWEDLKKAGF 403
           EDHRMAMAFAPA +  P++ I +PQVVSKSYP YWEDLK AGF
Sbjct: 362 EDHRMAMAFAPAVITFPKLLIADPQVVSKSYPGYWEDLKLAGF 404


Lambda     K      H
   0.320    0.135    0.391 

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: 540
Number of extensions: 10
Number of successful extensions: 1
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: 408
Length of database: 410
Length adjustment: 31
Effective length of query: 377
Effective length of database: 379
Effective search space:   142883
Effective search space used:   142883
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 351714 BT2186 (3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file))
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.15770.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    6.1e-98  314.3   0.0    7.1e-90  287.7   0.0    2.0  2  lcl|FitnessBrowser__Btheta:351714  BT2186 3-phosphoshikimate 1-carb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351714  BT2186 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.8e-10   2.8e-10       2      45 ..      15      58 ..      14      60 .. 0.95
   2 !  287.7   0.0   7.1e-90   7.1e-90      68     410 ..      59     400 ..      56     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.8e-10
                          TIGR01356  2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealr 45
                                        i++p sKSis+Ral++ aL++g    +nl +++Dt+++++al 
  lcl|FitnessBrowser__Btheta:351714 15 TIQLPASKSISNRALIINALGKGIYPPENLSDCDDTQVMIKALT 58
                                       589**************************************986 PP

  == domain 2  score: 287.7 bits;  conditional E-value: 7.1e-90
                          TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkg 142
                                        e ++++d+  +Gt++R+lt+ l+++sge ++tg  ++++RPi+ lv+aLrelgaeie++++eg++Pl+i+g  lkg
  lcl|FitnessBrowser__Btheta:351714  59 EGKETIDIMAAGTAMRFLTAYLSATSGERIITGTARMQQRPIQILVNALRELGAEIEYTHNEGYPPLRIKGAeLKG 134
                                        56789******************************************************************98999 PP

                          TIGR01356 143 givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk 218
                                        + ++l+g++SsQy+sall+ +p+ +++ tl+++g ++isrpyi++tL+l+++fg ++  +  ++i+v ++  y++ 
  lcl|FitnessBrowser__Btheta:351714 135 NEITLKGNVSSQYISALLMIGPVLKDGLTLHLTG-EIISRPYINLTLQLMQDFGAKAAWTSPSSISVAPQP-YQSV 208
                                        **********************999999999988.************************9999****9975.8888 PP

                          TIGR01356 219 evevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdi 293
                                         ++ve+D S+A+++  +aa+++e e+++ +l  ns qgd + ++v++++G + e++ +  v+++++ k+ + + ++
  lcl|FitnessBrowser__Btheta:351714 209 PFTVESDWSAASYWYQIAALSPEaEIELLGLFRNSYQGDSRGAEVFSRLGITTEFTPK-GVKIKKTGKT-PERLEE 282
                                        8*********************************************************.7***975444.44558* PP

                          TIGR01356 294 dvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkk.kelkg.avv 367
                                        d+ +++D+++t+ v +a+ + + r +++++l++kE+dRiaa+++eL+klG  +ee +d++l   ++  e +  +v+
  lcl|FitnessBrowser__Btheta:351714 283 DFVDIPDLAQTFVVTCALLNIPFRFTGLQSLKIKETDRIAALRTELKKLGYLIEEENDSVLMWNGErCEPEAvPVI 358
                                        **********************************************************98887665344443599* PP

                          TIGR01356 368 dtydDHRiamalavlglaaegeveiedaecvaksfPeFfevle 410
                                         ty+DHR+ama+a + +    ++ i d+++v+ks+P ++e+l+
  lcl|FitnessBrowser__Btheta:351714 359 ATYEDHRMAMAFAPAVITFP-KLLIADPQVVSKSYPGYWEDLK 400
                                        **************999998.*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (410 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.62
//
[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