Aligments for a candidate for proB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for proB in Caulobacter crescentus NA1000

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate CCNA_00316 CCNA_00316 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__Caulo:CCNA_00316
          Length = 377

 Score =  282 bits (721), Expect = 1e-80
 Identities = 161/365 (44%), Positives = 228/365 (62%), Gaps = 7/365 (1%)

Query: 4   SQTLVVKLGTSVLTGGSR-RLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGY 62
           ++ +V K+G+++L        NRA +       A L AAG ++++V+SGA+A GR  LG 
Sbjct: 12  ARRIVFKVGSALLVDAETGAANRAWLEAFCADAADLRAAGKQVLVVSSGAVALGRRRLGL 71

Query: 63  PELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLR 122
                T+  KQ  AA GQS L++ WE+ F  +GI V Q+LLTR D E R R+LNAR T  
Sbjct: 72  TGRKTTLPEKQAAAAAGQSLLMRAWEEAFEPHGIGVAQILLTRDDTEMRRRWLNARATTE 131

Query: 123 ALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSN 182
            L+   +VPV+NEND V T EI+ GDND L+A  A +AGAD L+LL+D  GLYTADPR N
Sbjct: 132 TLMGLGVVPVVNENDTVVTEEIRYGDNDRLAARVAQMAGADLLVLLSDIDGLYTADPRKN 191

Query: 183 PQAELIKDVYGIDDALRAIA--GDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
           P+A+ I  V  I   +  +A   ++ +G+GTGGM+TK+ AA +A  AG  T+I  GS+P 
Sbjct: 192 PKAQHIPRVSEITPEIAGMAEGANAAAGVGTGGMATKIAAARIARAAGCATLITLGSRPR 251

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFGA-PPAGEITVDEGATAAILERGSSLLPKG 299
            +  +  G    TL  A A+P    K WI G+  P G +TVD GA +A+L  G SLLP G
Sbjct: 252 PLAAIAAG-EKATLIEAGASPAAAYKAWIAGSLAPQGWVTVDAGAASALL-AGKSLLPAG 309

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +++V G F +G+ +R+ +  GR++A G+ RY+S   +RIAG  S  I+A LG+  GP+ +
Sbjct: 310 VRAVEGPFDKGDAVRVRDENGREVARGLVRYDSADAQRIAGLRSDAIEAELGFTEGPM-I 368

Query: 360 HRDDM 364
           H DD+
Sbjct: 369 HADDL 373


Lambda     K      H
   0.318    0.135    0.384 

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: 384
Number of extensions: 23
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: 377
Length adjustment: 30
Effective length of query: 337
Effective length of database: 347
Effective search space:   116939
Effective search space used:   116939
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: 49 (23.5 bits)

Align candidate CCNA_00316 CCNA_00316 (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.15495.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-127  410.6   0.1   3.5e-127  410.4   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00316  CCNA_00316 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00316  CCNA_00316 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.4   0.1  3.5e-127  3.5e-127       1     362 [.      13     374 ..      13     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 410.4 bits;  conditional E-value: 3.5e-127
                             TIGR01027   1 kriVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQala 72 
                                           +riV+K+Gs++L++ ++   +r+ l++++++ a l++aG++v++vsSGava G ++Lgl+ r ++l ekQa+a
  lcl|FitnessBrowser__Caulo:CCNA_00316  13 RRIVFKVGSALLVDAETGaANRAWLEAFCADAADLRAAGKQVLVVSSGAVALGRRRLGLTGRKTTLPEKQAAA 85 
                                           59************9998799**************************************************** PP

                             TIGR01027  73 aVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDN 145
                                           a GQ+ Lm+++e++f+ +g+ vaQiLLtr+d ++r+r+lNar+t e+l+ lgvvp+vNENDtv +eei+ GDN
  lcl|FitnessBrowser__Caulo:CCNA_00316  86 AAGQSLLMRAWEEAFEPHGIGVAQILLTRDDTEMRRRWLNARATTETLMGLGVVPVVNENDTVVTEEIRYGDN 158
                                           ************************************************************************* PP

                             TIGR01027 146 DtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagss..gssvGTGGmrtKlea 216
                                           D+L+a va++ +AdlLvll+d+dgLy+adpr+np+A+ i++v+ei+ e+ ++a ++  +  vGTGGm+tK++a
  lcl|FitnessBrowser__Caulo:CCNA_00316 159 DRLAARVAQMAGADLLVLLSDIDGLYTADPRKNPKAQHIPRVSEITPEIAGMAEGAnaAAGVGTGGMATKIAA 231
                                           ****************************************************988754555************ PP

                             TIGR01027 217 aelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekg 289
                                           a++A +ag  ++i+ g++p  +a++++++ + tl+ea ++   + k+wi+  ++++G ++vd+ga++all+ g
  lcl|FitnessBrowser__Caulo:CCNA_00316 232 ARIARAAGCATLITLGSRPRPLAAIAAGE-KATLIEAGASPAAAYKAWIAGSLAPQGWVTVDAGAASALLA-G 302
                                           **********************9998886.57**************************************9.* PP

                             TIGR01027 290 ksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                           ksLlpagv +veg F++g++v++++e+g+e+++glv+y+s++ ++i+gl+s+ ie++Lg++ +   +h+d+l+
  lcl|FitnessBrowser__Caulo:CCNA_00316 303 KSLLPAGVRAVEGPFDKGDAVRVRDENGREVARGLVRYDSADAQRIAGLRSDAIEAELGFT-EGPMIHADDLA 374
                                           ************************************************************9.6789****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (377 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 6.64
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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