Alignments for a candidate for proB in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Chlorobium phaeobacteroides BS1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_012474327.1 CPHAMN1_RS04460 glutamate 5-kinase

Query= reanno::Pedo557:CA265_RS20855
         (359 letters)



>NCBI__GCF_000020545.1:WP_012474327.1
          Length = 361

 Score =  356 bits (913), Expect = e-103
 Identities = 175/353 (49%), Positives = 252/353 (71%), Gaps = 1/353 (0%)

Query: 5   YKKIVVKVGSNVITQANGLPDEGRIKHLVNQLADIKKQGIEVILVSSGAVASGRSLIKVS 64
           Y+KIV+KVG+NVIT   G  D   ++ LV+Q+++++ +G+EV LVSSGAVA+GR+ + ++
Sbjct: 6   YQKIVIKVGTNVITDNRGELDLQILEELVSQISELRSRGVEVFLVSSGAVAAGRAKVTLN 65

Query: 65  EKQDAVTTRQLLAAIGQVKLINTYANFFAAHAIQCAQVLVTKEDFRDRAHYLNMKNCLQI 124
           E    +  RQ+L++ GQ++LINTY + F  HA++ AQ+LVTK DFRDR HYLN++ CL+ 
Sbjct: 66  EDLSPIAARQVLSSTGQIRLINTYTDLFEKHALKIAQILVTKSDFRDRQHYLNIRTCLES 125

Query: 125 LLQNEVIPVVNENDVVSVTELMFTDNDELAGLIASMLNADALIILSNVNGIYNGDPKVEG 184
           L++ ++IPV+NEND VSVTELMFTDNDEL+GLIASM++ DA IILS+++G+++     + 
Sbjct: 126 LMKYDIIPVINENDAVSVTELMFTDNDELSGLIASMMHVDAYIILSHIDGLFDLSGDEKP 185

Query: 185 SAVIEEINGSVANLASFIQTGKSQFGRGGMITKSTMAQKVAKLGITVHIANGTKDNVLTS 244
             +I  ++ +  +   +I+ GKS+FGRGGM+TK  +AQK+++ GI VHIANG    +L  
Sbjct: 186 PRLITSVDIATEHFHQYIKPGKSEFGRGGMLTKCHIAQKLSRFGIAVHIANGQTPGILLD 245

Query: 245 LLNNELVHTRFVPEKSKSGKKKWIAHSETAATGVVKLNDGAKTVLTS-SKATSLLPVGII 303
           LL+ +   TRFVP+K   G+K+WIAHSE    G V +N GA+  L S  +A SLLPVGI 
Sbjct: 246 LLDGKAAGTRFVPQKPVYGRKRWIAHSEGLEKGAVTINTGAEKALRSQERANSLLPVGIE 305

Query: 304 EIQTDFLKGDIIKIVDEKNNLIGLGIAEYGSDKARERIGQKKQKALVHYDYFY 356
            +   F KGDII+I  E    IG G+A Y S++ +E +G+K  K L+HYDY Y
Sbjct: 306 SVLGAFYKGDIIRICSENEETIGYGMARYSSEETKELMGKKGAKPLIHYDYLY 358


Lambda     K      H
   0.316    0.133    0.358 

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: 352
Number of extensions: 13
Number of successful extensions: 2
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: 359
Length of database: 361
Length adjustment: 29
Effective length of query: 330
Effective length of database: 332
Effective search space:   109560
Effective search space used:   109560
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_012474327.1 CPHAMN1_RS04460 (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.19545.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-100  321.1   0.0   5.8e-100  320.9   0.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474327.1  CPHAMN1_RS04460 glutamate 5-kina


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474327.1  CPHAMN1_RS04460 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.9   0.0  5.8e-100  5.8e-100       1     340 [.       7     347 ..       7     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 320.9 bits;  conditional E-value: 5.8e-100
                                 TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 
                                               ++iV+K+G++++t++ g+l++++l+elv+q+++l++ G ev +vsSGavaaG ++  l+e    +a +Q
  lcl|NCBI__GCF_000020545.1:WP_012474327.1   7 QKIVIKVGTNVITDNRGELDLQILEELVSQISELRSRGVEVFLVSSGAVAAGRAKVTLNEDLSPIAARQ 75 
                                               68******************************************************************* PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               +l++ GQ rL+++y++lf+++ lk+aQiL t++d+++r++ylN r+ le+l++ +++p++NEND+v+v+
  lcl|NCBI__GCF_000020545.1:WP_012474327.1  76 VLSSTGQIRLINTYTDLFEKHALKIAQILVTKSDFRDRQHYLNIRTCLESLMKYDIIPVINENDAVSVT 144
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207
                                               e+ f DND+Ls l+a++++ d+ ++l+ +dgL+d    ++p  +li  v+ ++e+++++   + s++G 
  lcl|NCBI__GCF_000020545.1:WP_012474327.1 145 ELMFTDNDELSGLIASMMHVDAYIILSHIDGLFDLSGDEKP-PRLITSVDIATEHFHQYIKPGKSEFGR 212
                                               ************************************97777.59***********99999888899*** PP

                                 TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaase.akGki 275
                                               GGm tK + a+  sr g+ v ia+g++p  ++dll+++a gt f ++k  +  rk+wi++ +  +kG++
  lcl|NCBI__GCF_000020545.1:WP_012474327.1 213 GGMLTKCHIAQKLSRFGIAVHIANGQTPGILLDLLDGKAAGTRFVPQKP-VYGRKRWIAHSEGlEKGAV 280
                                               **********************************************976.999******9875278*** PP

                                 TIGR01027 276 ivdegaeeallekgks..LlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglks 340
                                               +++ gae+al++++++  Llp+g+ +v g F +g++++i++e+ ++ig g+++yssee ++++g+k 
  lcl|NCBI__GCF_000020545.1:WP_012474327.1 281 TINTGAEKALRSQERAnsLLPVGIESVLGAFYKGDIIRICSENEETIGYGMARYSSEETKELMGKKG 347
                                               **********98875444**********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (361 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: 00:00:00.01
# Mc/sec: 12.02
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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