Alignments for a candidate for aroA in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Thiomicrorhabdus chilensis DSM 12352

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_028486633.1 B076_RS0106685 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000483485.1:WP_028486633.1
          Length = 446

 Score =  438 bits (1126), Expect = e-127
 Identities = 235/433 (54%), Positives = 301/433 (69%), Gaps = 10/433 (2%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   + G I VPGDKSISHR+++L AI+EG T V GFL GAD LA + A + MG  I+  
Sbjct: 10  PGGRIHGRIRVPGDKSISHRSIMLGAISEGTTTVTGFLEGADALATLQAFKDMGVQIEGP 69

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
           +  N+  + GVG+ GL+ P + +D GNSGT+ RLL+G+LAGQ F+  L GD+SL +RPMK
Sbjct: 70  DKGNV-TIHGVGLRGLKKPEKPMDMGNSGTSTRLLAGILAGQDFDCELVGDASLSKRPMK 128

Query: 127 RIIDPLTLMGAKIDST-GNVPPLKIYGNPR-LTGIHYQLPMASAQVKSCLLLAGLYARGK 184
           R+ DPL +MGAKI++  G   P+KI G+ + L  I Y LPMASAQVKSC+LLAGLYA+GK
Sbjct: 129 RVTDPLAMMGAKIETAEGGTLPMKICGHGQTLKAIDYVLPMASAQVKSCVLLAGLYAQGK 188

Query: 185 TCITEPAPSRDHTERLLKHFHYT-----LQKDKQSICVSGGGKLKANDISIPGDISSAAF 239
           TC  EPAP+RDHTER+L  F Y      L   +   C+ GGG LKA  I +P DISSAAF
Sbjct: 189 TCAEEPAPTRDHTERMLNGFGYEVVSTRLDNSRTRACLQGGGSLKARHIDVPSDISSAAF 248

Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299
           F+VAA ++ GS + +  VG+NPTR GVI++LK+MGA+I + +  E   EP AD+ +R+A 
Sbjct: 249 FMVAAAVSEGSDLVIEHVGMNPTRTGVIDILKLMGANIVLENAHEVGGEPVADVHIRYAP 308

Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359
           L+GI+IP   VPL IDEFPVL +AAA A G+TVL  A ELRVKE+DRI  M D LQ +GI
Sbjct: 309 LQGIEIPESLVPLAIDEFPVLFVAAASATGQTVLSGAEELRVKESDRIQVMADALQAVGI 368

Query: 360 AAESLPDGVIIQGG--TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPN 417
            A   PDG++I GG  + +  E+ S+ DHRI+MA  VAG  A   V I +C NV TSFP 
Sbjct: 369 DAVPTPDGMVINGGQQSPQAAEIQSHHDHRISMAMTVAGLNAVSEVVIDDCANVNTSFPT 428

Query: 418 FVELANEVGMNVK 430
           FV L NEVGM ++
Sbjct: 429 FVSLMNEVGMQIE 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: 612
Number of extensions: 32
Number of successful extensions: 5
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: 446
Length adjustment: 32
Effective length of query: 406
Effective length of database: 414
Effective search space:   168084
Effective search space used:   168084
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_028486633.1 B076_RS0106685 (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.64409.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-128  413.8   0.6   4.1e-128  413.6   0.6    1.0  1  NCBI__GCF_000483485.1:WP_028486633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000483485.1:WP_028486633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.6   0.6  4.1e-128  4.1e-128       1     414 [.      16     438 ..      16     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 413.6 bits;  conditional E-value: 4.1e-128
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepe 70 
                                           g+i++pg+KSishR+++l+a++eg+t+vt++L+++D latl+a++++G+++e  +k++++i+gvg   lk pe
  NCBI__GCF_000483485.1:WP_028486633.1  16 GRIRVPGDKSISHRSIMLGAISEGTTTVTGFLEGADALATLQAFKDMGVQIEgPDKGNVTIHGVGLrgLKKPE 88 
                                           79**************************************************767********99888***** PP

                             TIGR01356  71 aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkg 142
                                           + +d+gnsGt++Rll g+la ++++++l gd sl+kRP++r++++L ++ga+ie +e  g+lP++i g+ +++
  NCBI__GCF_000483485.1:WP_028486633.1  89 KPMDMGNSGTSTRLLAGILAGQDFDCELVGDASLSKRPMKRVTDPLAMMGAKIETAE-GGTLPMKICGHgQTL 160
                                           ******************************************************988.69********98777 PP

                             TIGR01356 143 .givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkivvkggq 213
                                            +i ++ ++aS+Q+ks++lla+   l a++ +  +e+  +r+++e++L+ ++ + v+ + +++ ++  ++gg+
  NCBI__GCF_000483485.1:WP_028486633.1 161 kAIDYVLPMASAQVKSCVLLAG---LYAQGKTCAEEPAPTRDHTERMLNGFGYEVVSTRLDNSrTRACLQGGG 230
                                           8*********************...677888999999******************999988886788899999 PP

                             TIGR01356 214 kykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........d 277
                                           + k ++++v++D+SsAaff++aaa++++ ++++e++g+n+t+++  +i++L+ mGa++ +e+ +        d
  NCBI__GCF_000483485.1:WP_028486633.1 231 SLKARHIDVPSDISSAAFFMVAAAVSEGsDLVIEHVGMNPTRTG--VIDILKLMGANIVLENAHevggepvaD 301
                                           999999*********************99***************..788**************99******** PP

                             TIGR01356 278 vevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveel 349
                                           v ++    l+g+++ +  v+ +iDe+p+l v+aa A g+t++ ++eelRvkEsdRi+++a++L+++G+++ ++
  NCBI__GCF_000483485.1:WP_028486633.1 302 VHIR-YAPLQGIEIpESLVPLAIDEFPVLFVAAASATGQTVLSGAEELRVKESDRIQVMADALQAVGIDAVPT 373
                                           ****.568******99********************************************************* PP

                             TIGR01356 350 edgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           +dg++i+G++++ + a++++++DHRi ma++v+gl a +ev i+d + v++sfP F+ +++++g+
  NCBI__GCF_000483485.1:WP_028486633.1 374 PDGMVINGGQQSPQAAEIQSHHDHRISMAMTVAGLNAVSEVVIDDCANVNTSFPTFVSLMNEVGM 438
                                           *************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (446 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.94
//
[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