Alignments for a candidate for aroA in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Xenophilus azovorans DSM 13620

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate WP_038205562.1 Q392_RS09595 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase

Query= SwissProt::P24497
         (427 letters)



>NCBI__GCF_000745855.1:WP_038205562.1
          Length = 667

 Score =  412 bits (1058), Expect = e-119
 Identities = 236/434 (54%), Positives = 286/434 (65%), Gaps = 19/434 (4%)

Query: 3   SLTLQPIARVDGTVNLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSALGV 62
           SL + P+A   G V LPGSKS+SNR LLLAAL+ GTT + + LDSDD R ML AL+ LG 
Sbjct: 6   SLDIPPLAGAAGRVRLPGSKSISNRVLLLAALSAGTTTIHDALDSDDTRVMLEALAQLGC 65

Query: 63  HYVLSSDRTRCEVTGTGGPLQAGSALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPRMK 122
                    R  + G GG LQ   A  LFLGNAGTAMRPL AAL L   D  L+G PRM 
Sbjct: 66  GVTHEGPVLR--IAGLGGRLQNTQA-SLFLGNAGTAMRPLTAALALLGGDFELSGVPRMH 122

Query: 123 ERPIGHLVDALRQGGAQIDYLEQENYPPLRLRGGFTG-----GDVEVDGSVSSQFLTALL 177
           ERPIG LVDAL Q G  +DYL    YPPLR+R            + V G VSSQFLTALL
Sbjct: 123 ERPIGDLVDALVQLGCHVDYLGNPGYPPLRIRPAALDTLQLDAPIRVRGDVSSQFLTALL 182

Query: 178 MASPLAPQDTVIAIK--GELVSRPYIDITLHLMKTFGVEVENQAYQRFIVRGNQQYQSPG 235
           MA PLA Q   IAI+  GEL+S+PYI+ITL+L+  FG+ V+ + +QRF++    +Y SPG
Sbjct: 183 MALPLAAQHQAIAIEVVGELISKPYIEITLNLLARFGIAVQREGWQRFVIPAGSRYASPG 242

Query: 236 DYLVEGDASSASYFLAAGAIKG---GTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGED 292
           +  VE DASSASYF+A GAI       +++ G+G +S+QGDIRF +    MGA +  G +
Sbjct: 243 EIHVEADASSASYFIALGAIAAPASSPLRIDGVGADSIQGDIRFTEAARAMGAVIDSGPN 302

Query: 293 YIACTRGE--LNAIDMDMNHIPDAAMTIATAALFARGTTTLRNIYNWRVKETDRLFAMAT 350
           ++A  RG   L A+DMD N IPDAAMT+A  AL+A G +TLRNI +WRVKETDR+ AMA 
Sbjct: 303 WLAVHRGAWPLKALDMDANAIPDAAMTLAVMALYADGPSTLRNIASWRVKETDRIDAMAA 362

Query: 351 ELRKVGAEVEEGEDYIRITPPLT--LQFAEIGTYNDHRMAMCFSLVALSD--TPVTILDP 406
           ELRK+GA VE G D+IR+ P        A I TY+DHR+AMCFSL A +    PV ILDP
Sbjct: 363 ELRKLGASVEAGPDFIRVMPLPAGGWHRASIHTYDDHRVAMCFSLAAFNPDALPVRILDP 422

Query: 407 KCTAKTFPDYFGQL 420
           KC  KTFPDYF  L
Sbjct: 423 KCVGKTFPDYFETL 436


Lambda     K      H
   0.319    0.135    0.389 

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: 667
Number of extensions: 38
Number of successful extensions: 8
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: 427
Length of database: 667
Length adjustment: 35
Effective length of query: 392
Effective length of database: 632
Effective search space:   247744
Effective search space used:   247744
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: 52 (24.6 bits)

Align candidate WP_038205562.1 Q392_RS09595 (bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase)
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.3058027.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-131  422.9   0.0   8.1e-131  422.6   0.0    1.1  1  NCBI__GCF_000745855.1:WP_038205562.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038205562.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.6   0.0  8.1e-131  8.1e-131       1     412 [.      17     439 ..      17     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 422.6 bits;  conditional E-value: 8.1e-131
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lkepeae 72 
                                           g++++pgsKSis+R+lllaaL+ g+t++++ L+s+Dt+++leal +lG  v++e+ +l i g gg l+  +a+
  NCBI__GCF_000745855.1:WP_038205562.1  17 GRVRLPGSKSISNRVLLLAALSAGTTTIHDALDSDDTRVMLEALAQLGCGVTHEGPVLRIAGLGGrLQNTQAS 89 
                                           789*************************************************99**********9999999** PP

                             TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp....lk 141
                                           l lgn+Gt++R+lt++lal++g+++l+g +++++RPi++lv+aL +lg+++++  + g++Pl+i+      l+
  NCBI__GCF_000745855.1:WP_038205562.1  90 LFLGNAGTAMRPLTAALALLGGDFELSGVPRMHERPIGDLVDALVQLGCHVDYLGNPGYPPLRIRPAaldtLQ 162
                                           ****************************************************************987788778 PP

                             TIGR01356 142 g.givelsgsaSsQyksalllaap..lalqavtleivgeklisrpyieitLkllksfgveveeederkivvkg 211
                                           + + ++++g++SsQ+++all+a p   + qa  +e+vg +lis+pyieitL+ll++fg+ v++e  +++v++ 
  NCBI__GCF_000745855.1:WP_038205562.1 163 LdAPIRVRGDVSSQFLTALLMALPlaAQHQAIAIEVVG-ELISKPYIEITLNLLARFGIAVQREGWQRFVIPA 234
                                           8899********************54445566677777.*************************99******* PP

                             TIGR01356 212 gqkykqk.evevegDaSsAafflaaaaitge...evtvenlgenstqgdkaiiivLeemGadveveeqrdvev 280
                                           g  y+++ e++ve+DaSsA++f+a++ai+      +++ ++g++s qgd ++ +  ++mGa ++   + ++ v
  NCBI__GCF_000745855.1:WP_038205562.1 235 GSRYASPgEIHVEADASSASYFIALGAIAAPassPLRIDGVGADSIQGDIRFTEAARAMGAVIDSGPN-WLAV 306
                                           *9988888********************8765679*********************************.9*** PP

                             TIGR01356 281 eg.asklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledg 352
                                           ++ a  lk+++  +d++ ++D+++tlav+a++A+g+++++ni+++RvkE+dRi a+a+eL+klG++ve ++d+
  NCBI__GCF_000745855.1:WP_038205562.1 307 HRgAWPLKALD--MDANAIPDAAMTLAVMALYADGPSTLRNIASWRVKETDRIDAMAAELRKLGASVEAGPDF 377
                                           96455566555..************************************************************ PP

                             TIGR01356 353 llieGkk.kelkgavvdtydDHRiamalavlglaae.geveiedaecvaksfPeFfevleql 412
                                           + + +     ++ a+++tydDHR+am+++++++  +  +v+i d++cv k+fP++fe l ++
  NCBI__GCF_000745855.1:WP_038205562.1 378 IRVMPLPaGGWHRASIHTYDDHRVAMCFSLAAFNPDaLPVRILDPKCVGKTFPDYFETLFSV 439
                                           *****9999*************************9978*******************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (667 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: 20.22
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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