GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Trichormus variabilis ATCC 29413

Align (R)-citramalate synthase; EC 2.3.3.21 (uncharacterized)
to candidate WP_011319948.1 AVA_RS16285 citramalate synthase

Query= curated2:P74269
         (547 letters)



>NCBI__GCF_000204075.1:WP_011319948.1
          Length = 577

 Score =  753 bits (1945), Expect = 0.0
 Identities = 384/560 (68%), Positives = 431/560 (76%), Gaps = 36/560 (6%)

Query: 8   LWLYDTTLRDGAQREGISLSLTDKLTIARRLDQLGIPFIEGGWPGANPKDVQFFWQLQEE 67
           +WLYDTTLRDG QREG+S+S  DKL IA RLDQLGIPFIEGGWPGANPKDVQFFWQLQE+
Sbjct: 9   IWLYDTTLRDGTQREGLSISTEDKLRIAHRLDQLGIPFIEGGWPGANPKDVQFFWQLQED 68

Query: 68  PLEQAEIVAFCSTRRPHKAVETDKMLQAILSAGTRWVTIFGKSWDLHVLEGLQTSLAENL 127
           PL+ ++IVAFCSTRRPH     + MLQ IL+AG+ WVTIFGKSWDLHV  GL+T+L ENL
Sbjct: 69  PLKLSQIVAFCSTRRPHTHAADEPMLQDILAAGSSWVTIFGKSWDLHVTTGLKTTLEENL 128

Query: 128 AMISDTIAYLRSQGRRVIYDAEHWFDGYRANPDYALATLATAQQAGAEWLVMCDTNGGTL 187
           AMI DTI + RSQGRRVIYDAEHWFDGY+ N DYAL TL  A  AGAEWLV+CDTNGGTL
Sbjct: 129 AMIRDTIEFFRSQGRRVIYDAEHWFDGYKHNRDYALQTLKAAMAAGAEWLVLCDTNGGTL 188

Query: 188 PGQISEI---TTKVRRSLG-LDGQSDRQ-----------------------------PQL 214
           P ++S+I     KV R  G ++ + D+                              PQ+
Sbjct: 189 PHEVSQIVQDVVKVTRDWGRINSKLDQSGQVVSEEVEKSTNSLPNTQYPIPNLPFPIPQI 248

Query: 215 GIHAHNDSGTAVANSLLAVEAGATMVQGTINGYGERCGNANLCTLIPNLQLKLDYDCIEP 274
           GIH HNDS  AVAN+L AV AGATMVQGTINGYGERCGNANLC+LIPNLQLKL Y CI  
Sbjct: 249 GIHTHNDSDMAVANALAAVMAGATMVQGTINGYGERCGNANLCSLIPNLQLKLGYSCITE 308

Query: 275 EKLAHLTSTSRLISEIVNLAPDDHAPFVGRSAFAHKGGIHVSAVQRNPFTYEHIAPNLVG 334
            +L  L   SR +SE+VNLAPD+HAPFVGRSAFAHKGGIHVSAV+RNP TYEHI P  VG
Sbjct: 309 HQLGQLAEASRFVSEVVNLAPDEHAPFVGRSAFAHKGGIHVSAVERNPLTYEHIQPEQVG 368

Query: 335 NERRIVVSEQAGLSNVLSKAELFGIALDRQNPACRTILATLKDLEQQGYQFEAAEASFEL 394
           N RRIV+SEQ+G+SNVL+KA  FGI LD+Q P  + IL  LK+LE +GYQFEAAEASF L
Sbjct: 369 NRRRIVISEQSGISNVLAKARTFGIELDKQTPEAKQILQRLKELESEGYQFEAAEASFAL 428

Query: 395 LMRQAMGDRQPLFLVQGFQVHCDLLTPAENPAYRNALATVKVTVNGQNILEVAEGNGPVS 454
           LM +A+G RQ  F V+GFQVHCDL+   E     NALATVKV VNG+NILE AEGNGPV+
Sbjct: 429 LMYEALGGRQQFFEVKGFQVHCDLV---EGKEMTNALATVKVAVNGKNILEAAEGNGPVA 485

Query: 455 ALDQALRKALTRFYPQIADFHLTDYKVRILDGGAGTSAKTRVLVESSNGDRRWTTVGVSG 514
           ALD ALRKAL  FYPQ+A F LTDYKVRILDG  GTSAKTR LVES NG +RWTTVGVS 
Sbjct: 486 ALDAALRKALVNFYPQLATFELTDYKVRILDGHTGTSAKTRALVESGNGYQRWTTVGVSP 545

Query: 515 NILEASYQAVVEGIEYGLRL 534
           NIL ASYQAVVEG+EYGL L
Sbjct: 546 NILAASYQAVVEGLEYGLLL 565


Lambda     K      H
   0.318    0.134    0.393 

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: 909
Number of extensions: 28
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 547
Length of database: 577
Length adjustment: 36
Effective length of query: 511
Effective length of database: 541
Effective search space:   276451
Effective search space used:   276451
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_011319948.1 AVA_RS16285 (citramalate synthase)
to HMM TIGR00977 (cimA: citramalate synthase (EC 2.3.1.182))

# 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/TIGR00977.hmm
# target sequence database:        /tmp/gapView.2700161.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00977  [M=526]
Accession:   TIGR00977
Description: citramal_synth: citramalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-262  858.0   0.1   5.3e-262  855.6   0.1    1.8  1  NCBI__GCF_000204075.1:WP_011319948.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011319948.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  855.6   0.1  5.3e-262  5.3e-262       2     520 ..       9     566 ..       8     572 .. 0.99

  Alignments for each domain:
  == domain 1  score: 855.6 bits;  conditional E-value: 5.3e-262
                             TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 
                                           ++lydttlrdG+q+eG+s+s edk+ria++ld+lGi++ieGGwpganpkdv+ff++++e +lk  ++vaf+st
  NCBI__GCF_000204075.1:WP_011319948.1   9 IWLYDTTLRDGTQREGLSISTEDKLRIAHRLDQLGIPFIEGGWPGANPKDVQFFWQLQEDPLKLSQIVAFCST 81 
                                           8************************************************************************ PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                           rrp+ +  ++++lq ++ a++ +vtifGkswdlhv+ +lkttleenl+mi dt+e++++++++viydaeh+fd
  NCBI__GCF_000204075.1:WP_011319948.1  82 RRPHTHAADEPMLQDILAAGSSWVTIFGKSWDLHVTTGLKTTLEENLAMIRDTIEFFRSQGRRVIYDAEHWFD 154
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrl........................ 196
                                           Gyk n++yal+tlk+a  aGa+wlvl+dtnGGtlphe+++i+++v k                          
  NCBI__GCF_000204075.1:WP_011319948.1 155 GYKHNRDYALQTLKAAMAAGAEWLVLCDTNGGTLPHEVSQIVQDVVKVTrdwgrinskldqsgqvvseeveks 227
                                           ********************************************99888899********************* PP

                             TIGR00977 197 ................kdpqlGihahndsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlk 253
                                                             pq+Gih+hnds++avan+l+av aGa++vqGtinG+GercGnanlcslipnlqlk
  NCBI__GCF_000204075.1:WP_011319948.1 228 tnslpntqypipnlpfPIPQIGIHTHNDSDMAVANALAAVMAGATMVQGTINGYGERCGNANLCSLIPNLQLK 300
                                           *************99999******************************************************* PP

                             TIGR00977 254 lgldviekenlkkltevarlvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrki 326
                                           lg+ +i + +l +l e +r+v+e+vnla+de++p+vG+safahkGG+hvsav+rnp tyehi+pe vGn+r+i
  NCBI__GCF_000204075.1:WP_011319948.1 301 LGYSCITEHQLGQLAEASRFVSEVVNLAPDEHAPFVGRSAFAHKGGIHVSAVERNPLTYEHIQPEQVGNRRRI 373
                                           ************************************************************************* PP

                             TIGR00977 327 vvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgf 399
                                           v+se++G snvl k++ +Gie+d+++p+ ++il+++kele +Gy+feaaeas+ ll+ +alG r+++fev+gf
  NCBI__GCF_000204075.1:WP_011319948.1 374 VISEQSGISNVLAKARTFGIELDKQTPEAKQILQRLKELESEGYQFEAAEASFALLMYEALGGRQQFFEVKGF 446
                                           ************************************************************************* PP

                             TIGR00977 400 rvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnes 472
                                           +v++++   +  +++a+atv+v+v+g+++l+aaeGnGpv ald alrkal +fyp+l+ ++ltdykvril+++
  NCBI__GCF_000204075.1:WP_011319948.1 447 QVHCDLVEGK-EMTNALATVKVAVNGKNILEAAEGNGPVAALDAALRKALVNFYPQLATFELTDYKVRILDGH 518
                                           ******9988.689*********************************************************** PP

                             TIGR00977 473 aGtsaktrvliessdGkrrwgtvGvseniieasytallesieyklrkd 520
                                           +Gtsaktr l+es +G +rw+tvGvs+ni+ asy+a++e++ey+l + 
  NCBI__GCF_000204075.1:WP_011319948.1 519 TGTSAKTRALVESGNGYQRWTTVGVSPNILAASYQAVVEGLEYGLLLH 566
                                           ********************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (577 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.22
//
[ok]

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

Links

Downloads

Related tools

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