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.11947.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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.02
//
[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:

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:

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:

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:

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