Alignments for a candidate for aroA in Thiothrix lacustris DSM 21227

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Thiothrix lacustris DSM 21227

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_028489167.1 Q394_RS0109965 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000621325.1:WP_028489167.1
          Length = 440

 Score =  451 bits (1160), Expect = e-131
 Identities = 229/430 (53%), Positives = 302/430 (70%), Gaps = 1/430 (0%)

Query: 1   MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60
           + +   P   L G + VPGDKSISHR+++L ++AEG T V GFL G D L  ++A + MG
Sbjct: 8   LQFNVQPGGSLHGTVRVPGDKSISHRSIMLGSLAEGTTHVSGFLQGEDCLCTLNAFRSMG 67

Query: 61  ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120
            +I    D+  + + GVG+ GLQAP   L+ GNSGT++RL+SGL++GQ F+  +TGD+SL
Sbjct: 68  VAIDGPTDDGKVTIHGVGLHGLQAPAGDLEMGNSGTSMRLMSGLMSGQAFDVRMTGDASL 127

Query: 121 QRRPMKRIIDPLTLMGAKIDSTG-NVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGL 179
            +RPMKR+  PL  MGA ID+T    PPL ++G  +L GIHY +P+ASAQVKS LLLAGL
Sbjct: 128 SKRPMKRVTVPLASMGAVIDATEIGTPPLLVHGGSKLQGIHYDMPVASAQVKSSLLLAGL 187

Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAF 239
           YA+G+T + EPAP+RDHTER+L+ F Y ++ D   I + GGGKL A DI +P DISSAAF
Sbjct: 188 YAQGETSVIEPAPTRDHTERMLRGFGYAVKTDGNHISLQGGGKLTATDIDVPSDISSAAF 247

Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299
           F+V A+I  GS + +  VG+NPTR GVI++L++MGA++E+ +  E   EP AD+ VR A 
Sbjct: 248 FMVGASIAAGSDLTIEHVGMNPTRTGVIDILRLMGANLEILNEREVGGEPVADVRVRAAP 307

Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359
           LKGI IP   VPL IDEFP L IAAA A+G+TVL  A ELRVKE+DRI  M DGL   G+
Sbjct: 308 LKGIQIPEALVPLAIDEFPALFIAAAFAEGQTVLTGAEELRVKESDRIQVMADGLIACGV 367

Query: 360 AAESLPDGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFV 419
            A+  PDG+II+ G   GG ++S+ DHRIAM+FA+A   A  P+ I +C NV TSFP FV
Sbjct: 368 DAQPTPDGIIIKPGNFTGGTIDSHGDHRIAMSFAMAALRATQPITINDCANVNTSFPGFV 427

Query: 420 ELANEVGMNV 429
            LA   G+ +
Sbjct: 428 GLAAGAGVRI 437


Lambda     K      H
   0.318    0.137    0.392 

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: 629
Number of extensions: 25
Number of successful extensions: 2
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: 438
Length of database: 440
Length adjustment: 32
Effective length of query: 406
Effective length of database: 408
Effective search space:   165648
Effective search space used:   165648
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: 51 (24.3 bits)

Align candidate WP_028489167.1 Q394_RS0109965 (3-phosphoshikimate 1-carboxyvinyltransferase)
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.10926.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-128  413.6   0.0   4.9e-128  413.4   0.0    1.0  1  lcl|NCBI__GCF_000621325.1:WP_028489167.1  Q394_RS0109965 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000621325.1:WP_028489167.1  Q394_RS0109965 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.4   0.0  4.9e-128  4.9e-128       1     410 [.      20     431 ..      20     436 .. 0.96

  Alignments for each domain:
  == domain 1  score: 413.4 bits;  conditional E-value: 4.9e-128
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.. 65 
                                               g +++pg+KSishR+++l++Laeg+t v ++L++eD+l tl+a+r++G+ +   + +++++i+gvg   
  lcl|NCBI__GCF_000621325.1:WP_028489167.1  20 GTVRVPGDKSISHRSIMLGSLAEGTTHVSGFLQGEDCLCTLNAFRSMGVAIDgPTdDGKVTIHGVGLhg 88 
                                               789*************************************************844599******99888 PP

                                 TIGR01356  66 lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPl 134
                                               l+ p   l++gnsGt++Rl++g+++ ++++v +tgd sl+kRP++r++ +L ++ga i+++e  g++Pl
  lcl|NCBI__GCF_000621325.1:WP_028489167.1  89 LQAPAGDLEMGNSGTSMRLMSGLMSGQAFDVRMTGDASLSKRPMKRVTVPLASMGAVIDATE-IGTPPL 156
                                               9**********************************************************988.69**** PP

                                 TIGR01356 135 aisgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202
                                                ++g++k+ gi++  + aS+Q+ks+llla+   l a++++ v+e+  +r+++e++L  ++ +   v+ +
  lcl|NCBI__GCF_000621325.1:WP_028489167.1 157 LVHGGSKLqGIHYDMPVASAQVKSSLLLAG---LYAQGETSVIEPAPTRDHTERMLRGFGYA---VKTD 219
                                               *****8888*********************...77889999999************999877...8887 PP

                                 TIGR01356 203 derkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                 ++i+++gg+k + ++++v++D+SsAaff++ a i+ + ++t+e++g+n+t+++  +i++L+ mGa++
  lcl|NCBI__GCF_000621325.1:WP_028489167.1 220 G-NHISLQGGGKLTATDIDVPSDISSAAFFMVGASIAAGsDLTIEHVGMNPTRTG--VIDILRLMGANL 285
                                               6.5*********88888********************999***************..788********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               e+ ++r        dv+v+ a  lkg+++ ++ v+ +iDe+p+l ++aafAeg+t+++++eelRvkEsd
  lcl|NCBI__GCF_000621325.1:WP_028489167.1 286 EILNERevggepvaDVRVR-AAPLKGIQIpEALVPLAIDEFPALFIAAAFAEGQTVLTGAEELRVKESD 353
                                               *******************.779******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399
                                               Ri+++a+ L + Gv++++++dg++i++++  + g+++d+++DHRiam++a+++l+a ++++i+d + v+
  lcl|NCBI__GCF_000621325.1:WP_028489167.1 354 RIQVMADGLIACGVDAQPTPDGIIIKPGN--FTGGTIDSHGDHRIAMSFAMAALRATQPITINDCANVN 420
                                               ****************************5..************************************** PP

                                 TIGR01356 400 ksfPeFfevle 410
                                               +sfP F+ +++
  lcl|NCBI__GCF_000621325.1:WP_028489167.1 421 TSFPGFVGLAA 431
                                               ******98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (440 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: 10.04
//
[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