Alignments for a candidate for aroA in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Steroidobacter denitrificans DSM 18526

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_066919891.1 ACG33_RS07105 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_001579945.1:WP_066919891.1
          Length = 442

 Score =  408 bits (1048), Expect = e-118
 Identities = 220/439 (50%), Positives = 295/439 (67%), Gaps = 10/439 (2%)

Query: 3   YQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGAS 62
           Y T P+    G+  +PGDKSISHRA++L +IAEG T+V GFL   D LA + A++ MG  
Sbjct: 4   YITQPAGRAGGDFRIPGDKSISHRALMLGSIAEGTTEVRGFLESEDCLATMKAMRTMGVR 63

Query: 63  IQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQR 122
           I+       L V GVG+ GL+ P  ALD GNSGTA+RL++GLL+GQ F++ L GD+SL +
Sbjct: 64  IEQFAP-GALRVYGVGLRGLRQPGRALDLGNSGTAMRLMTGLLSGQTFDSELIGDASLMK 122

Query: 123 RPMKRIIDPLTLMGAKIDSTGNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYAR 182
           RPM+R+  PL LMGA+ID+    PP++I G   L GI Y LP+ASAQVKS +LLAGLYA+
Sbjct: 123 RPMERVAAPLRLMGARIDTDQGRPPVRIGGAAALQGIRYTLPVASAQVKSAILLAGLYAQ 182

Query: 183 GKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIV 242
           G T + EP  +RDHTER+L+ F   +Q     + ++   +L A  + +PGD SSAAFF+V
Sbjct: 183 GATMLIEPGITRDHTERMLQSFGCPVQAAHGEVHMTPVERLVARSLEVPGDFSSAAFFMV 242

Query: 243 AATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKG 302
           A +I  G+ + L  VGVNPTR G++++L +MGAD+ + ++     EP ADI VR +RL+G
Sbjct: 243 AGSIAAGNGLTLRGVGVNPTRTGLLDILALMGADLRLINHRSAGAEPVADIEVRPSRLQG 302

Query: 303 IDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAE 362
           I +P   VPL IDEFP L IAAA AQG+T +  A ELRVKE+DRIA M +GL  LG++ E
Sbjct: 303 IHVPEHLVPLAIDEFPALFIAAACAQGETRVTGAEELRVKESDRIAVMAEGLTALGVSCE 362

Query: 363 SLPDGVIIQGGTLE---------GGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKT 413
            LPDG+ IQG   E         GG ++S+ DHRIAMAFAVA   A   +RI +  NV T
Sbjct: 363 VLPDGIRIQGRPAEAPAGEAVFAGGTIDSHGDHRIAMAFAVASLRANAAIRIDDVANVAT 422

Query: 414 SFPNFVELANEVGMNVKGV 432
           SFP+F  +A   G++++ V
Sbjct: 423 SFPDFPAIATAAGLHLRAV 441


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: 600
Number of extensions: 24
Number of successful extensions: 3
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: 442
Length adjustment: 32
Effective length of query: 406
Effective length of database: 410
Effective search space:   166460
Effective search space used:   166460
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_066919891.1 ACG33_RS07105 (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.23153.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-125  402.8   0.1   9.8e-125  402.5   0.1    1.0  1  lcl|NCBI__GCF_001579945.1:WP_066919891.1  ACG33_RS07105 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066919891.1  ACG33_RS07105 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.5   0.1  9.8e-125  9.8e-125       1     408 [.      14     430 ..      14     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: 402.5 bits;  conditional E-value: 9.8e-125
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g+++ipg+KSishRal+l+++aeg+t+v+++L+seD+lat++a+r +G+++e+   + l + gvg   l
  lcl|NCBI__GCF_001579945.1:WP_066919891.1  14 GDFRIPGDKSISHRALMLGSIAEGTTEVRGFLESEDCLATMKAMRTMGVRIEQFaPGALRVYGVGLrgL 82 
                                               7899************************************************76699******998889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               ++p ++ldlgnsGt++Rl+tg+l+ + ++++l gd sl kRP+er+  +Lr +ga+i+  +  g++P++
  lcl|NCBI__GCF_001579945.1:WP_066919891.1  83 RQPGRALDLGNSGTAMRLMTGLLSGQTFDSELIGDASLMKRPMERVAAPLRLMGARIDTDQ--GRPPVR 149
                                               **********************************************************866..89**** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               i g   + gi +  + aS+Q+ksa+lla+   l a+++++++e+ i+r+++e++L++++     v+  +
  lcl|NCBI__GCF_001579945.1:WP_066919891.1 150 IGGAAALqGIRYTLPVASAQVKSAILLAG---LYAQGATMLIEPGITRDHTERMLQSFGCP---VQAAH 212
                                               ****7778*********************...778899****************9988765...77777 PP

                                 TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271
                                               + ++++++ +    +++ev+gD+SsAaff++a+ i+ +  +t++++g n+t+++  ++++L  mGad++
  lcl|NCBI__GCF_001579945.1:WP_066919891.1 213 G-EVHMTPVERLVARSLEVPGDFSSAAFFMVAGSIAAGnGLTLRGVGVNPTRTG--LLDILALMGADLR 278
                                               7.78888888755566********************999***************..888********** PP

                                 TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331
                                               + ++r        d+ev+ +s l+g++v ++ v+ +iDe+p+l ++aa+A+getr++++eelRvkEsdR
  lcl|NCBI__GCF_001579945.1:WP_066919891.1 279 LINHRsagaepvaDIEVR-PSRLQGIHVpEHLVPLAIDEFPALFIAAACAQGETRVTGAEELRVKESDR 346
                                               *99999************.899******99*************************************** PP

                                 TIGR01356 332 iaaiaeeLeklGveveeledgllieGkk.......kelkgavvdtydDHRiamalavlglaaegeveie 393
                                               ia++ae L++lGv++e+l+dg+ i+G+        + + g+++d+++DHRiama+av++l+a++ ++i+
  lcl|NCBI__GCF_001579945.1:WP_066919891.1 347 IAVMAEGLTALGVSCEVLPDGIRIQGRPaeapageAVFAGGTIDSHGDHRIAMAFAVASLRANAAIRID 415
                                               **************************99889988778899***************************** PP

                                 TIGR01356 394 daecvaksfPeFfev 408
                                               d + va+sfP+F   
  lcl|NCBI__GCF_001579945.1:WP_066919891.1 416 DVANVATSFPDFPAI 430
                                               ************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (442 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.56
//
[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