GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Rhizorhabdus wittichii RW1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_012050080.1 SWIT_RS19690 glutamate 5-kinase

Query= reanno::Korea:Ga0059261_3512
         (367 letters)



>NCBI__GCF_000016765.1:WP_012050080.1
          Length = 380

 Score =  495 bits (1274), Expect = e-145
 Identities = 270/369 (73%), Positives = 297/369 (80%), Gaps = 5/369 (1%)

Query: 4   FPPASCPRLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGAR 63
           F PA+CPRLVVKIGSALLVDP+G +RRDWL+G+ ADIA R RAGQ+IAVVSSGAIALGAR
Sbjct: 12  FTPAACPRLVVKIGSALLVDPDGRVRRDWLQGVVADIAERHRAGQRIAVVSSGAIALGAR 71

Query: 64  RLKLAKGGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNA 123
           RL L KGGRASLEDAQAAAATGQIALS  WAE+L A GLTAAQ+LVTLDDLEDRRRYLNA
Sbjct: 72  RLALPKGGRASLEDAQAAAATGQIALSHCWAELLHAEGLTAAQILVTLDDLEDRRRYLNA 131

Query: 124 AATLGRLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDR 183
           A+TL RLL LGVVPVINENDSVATAEIRFGDNDRLAAR+ QAADA GV+LLSDIDGLY  
Sbjct: 132 ASTLHRLLGLGVVPVINENDSVATAEIRFGDNDRLAARIGQAADAGGVILLSDIDGLYTA 191

Query: 184 NPAL-PGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANG 242
           NP   P A  +P V RID R+  MAD  SASGMGSGGM+SK+EAARIA  +G  LAI  G
Sbjct: 192 NPHRDPTARLVPEVARIDARIRAMADADSASGMGSGGMISKLEAARIAQRSGAHLAIITG 251

Query: 243 RVDRPLS---ADARHTVFLPEKRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAI 299
           + D PL+   AD R TVFL EK   ARKAWLAGRLTAKG I+VDAGA  AL +GRSLLA 
Sbjct: 252 KRDHPLAAFDADHRGTVFLGEKIGTARKAWLAGRLTAKGRIVVDAGAVGALAQGRSLLAA 311

Query: 300 GATAIRGMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTL 358
           GA  + G F RGD+V I  P+G  IARGL EYDA DA  I+G RS+   +ILGYAPRS L
Sbjct: 312 GAVRVEGRFARGDVVDIVAPDGQAIARGLIEYDAVDAAKIVGRRSNAHEQILGYAPRSAL 371

Query: 359 VHRNHMALL 367
           VHR+HM LL
Sbjct: 372 VHRDHMVLL 380


Lambda     K      H
   0.319    0.134    0.377 

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: 470
Number of extensions: 12
Number of successful extensions: 4
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: 367
Length of database: 380
Length adjustment: 30
Effective length of query: 337
Effective length of database: 350
Effective search space:   117950
Effective search space used:   117950
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: 50 (23.9 bits)

Align candidate WP_012050080.1 SWIT_RS19690 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.1958720.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-114  368.2   0.3   2.7e-114  368.0   0.3    1.0  1  NCBI__GCF_000016765.1:WP_012050080.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_012050080.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.0   0.3  2.7e-114  2.7e-114       2     362 ..      19     378 ..      18     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 368.0 bits;  conditional E-value: 2.7e-114
                             TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglper.pkklaekQalaa 73 
                                           r+VvK+Gs++L++++g+++r  l+ +v+++a++++aG+++ +vsSGa+a G+++L lp+   ++l++ Qa+aa
  NCBI__GCF_000016765.1:WP_012050080.1  19 RLVVKIGSALLVDPDGRVRRDWLQGVVADIAERHRAGQRIAVVSSGAIALGARRLALPKGgRASLEDAQAAAA 91 
                                           79*******************************************************9972568********* PP

                             TIGR01027  74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDND 146
                                            GQ +L + + +l++  gl+ aQiL t +dl++r+rylNa +tl++ll lgvvp++NEND+va++ei+fGDND
  NCBI__GCF_000016765.1:WP_012050080.1  92 TGQIALSHCWAELLHAEGLTAAQILVTLDDLEDRRRYLNAASTLHRLLGLGVVPVINENDSVATAEIRFGDND 164
                                           ************************************************************************* PP

                             TIGR01027 147 tLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkava.gssgssvGTGGmrtKleaae 218
                                           +L+a + +  +A   +ll+d+dgLy+a+p+++p+A+l++ev +i++ ++a+a ++s+s +G GGm +Kleaa+
  NCBI__GCF_000016765.1:WP_012050080.1 165 RLAARIGQAADAGGVILLSDIDGLYTANPHRDPTARLVPEVARIDARIRAMAdADSASGMGSGGMISKLEAAR 237
                                           ************************************************99983567888************** PP

                             TIGR01027 219 lAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgks 291
                                           +A+r+g +  i++g++ + +a + +  + gt+f  +k    +rk+w++  ++akG+i+vd+ga+ al + g+s
  NCBI__GCF_000016765.1:WP_012050080.1 238 IAQRSGAHLAIITGKRDHPLA-AFDADHRGTVFLGEKI-GTARKAWLAGRLTAKGRIVVDAGAVGALAQ-GRS 307
                                           ***************966665.6677889*****9877.68999***********************98.*** PP

                             TIGR01027 292 LlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                           Ll+ag v veg+F rg+vv+i+a++gq i++gl +y++ + +ki+g++s+  e++Lgy  ++  vhrd++v
  NCBI__GCF_000016765.1:WP_012050080.1 308 LLAAGAVRVEGRFARGDVVDIVAPDGQAIARGLIEYDAVDAAKIVGRRSNAHEQILGYAPRSALVHRDHMV 378
                                           *********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (380 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: 17.81
//
[ok]

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

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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