Alignments for a candidate for proB in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Prosthecochloris aestuarii DSM 271

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_012506126.1 PAES_RS07870 glutamate 5-kinase

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



>NCBI__GCF_000020625.1:WP_012506126.1
          Length = 363

 Score =  359 bits (922), Expect = e-104
 Identities = 185/353 (52%), Positives = 247/353 (69%), Gaps = 1/353 (0%)

Query: 5   YKKIVVKVGSNVITQANGLPDEGRIKHLVNQLADIKKQGIEVILVSSGAVASGRSLIKVS 64
           Y+KIVVKVG+NVIT A+G  +   +  L  Q+A +  QGIEV+LVSSGAV +GRS+I + 
Sbjct: 8   YRKIVVKVGTNVITNADGKLNLDILDQLTTQIARLCNQGIEVLLVSSGAVGAGRSIITLP 67

Query: 65  EKQDAVTTRQLLAAIGQVKLINTYANFFAAHAIQCAQVLVTKEDFRDRAHYLNMKNCLQI 124
                V  RQ+L++ GQ+KLINTYA+ FA H +  AQ+LVTK DFRDR HYLNM+ C   
Sbjct: 68  VGLPPVARRQVLSSTGQIKLINTYADLFARHGVTTAQILVTKSDFRDRQHYLNMRTCFSS 127

Query: 125 LLQNEVIPVVNENDVVSVTELMFTDNDELAGLIASMLNADALIILSNVNGIYNGDPKVEG 184
           L++  VIPV+NEND VSVTELMFTDNDEL+GLIASM+  DA IILS+V+G+++   K + 
Sbjct: 128 LIEQSVIPVINENDAVSVTELMFTDNDELSGLIASMMQVDAHIILSHVDGLFDLSKKKDN 187

Query: 185 SAVIEEINGSVANLASFIQTGKSQFGRGGMITKSTMAQKVAKLGITVHIANGTKDNVLTS 244
             VI +I+        FIQ GKS+FGRGGM+TK  +A+K+A  GI+VHIANG    +L  
Sbjct: 188 PEVIPQIDPEDTRFHKFIQPGKSEFGRGGMLTKCHIARKLAGFGISVHIANGRTPGILYD 247

Query: 245 LLNNELVHTRFVPEKSKSGKKKWIAHSETAATGVVKLNDGAKTVLTS-SKATSLLPVGII 303
           +++ + V T+F+ +K   G+K+W+AHSE    G V +N GA+  L S ++A SLLPVGI 
Sbjct: 248 IVSGKSVGTKFLAKKPTHGRKRWLAHSEGMEKGAVTINAGAEKALRSPTEANSLLPVGIE 307

Query: 304 EIQTDFLKGDIIKIVDEKNNLIGLGIAEYGSDKARERIGQKKQKALVHYDYFY 356
            ++  F KGDIIKI  E   +IG G+A Y S+K RE +G+  +K L+HYDY Y
Sbjct: 308 SVKGAFYKGDIIKICTENGEIIGYGMARYSSEKTRELLGKTGEKPLIHYDYLY 360


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: 398
Number of extensions: 10
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: 363
Length adjustment: 29
Effective length of query: 330
Effective length of database: 334
Effective search space:   110220
Effective search space used:   110220
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_012506126.1 PAES_RS07870 (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.27790.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.3e-96  307.9   0.0    6.4e-96  307.6   0.0    1.0  1  lcl|NCBI__GCF_000020625.1:WP_012506126.1  PAES_RS07870 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020625.1:WP_012506126.1  PAES_RS07870 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.6   0.0   6.4e-96   6.4e-96       2     341 ..      10     350 ..       9     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 307.6 bits;  conditional E-value: 6.4e-96
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQa 70 
                                               +iVvK+G++++t+ +gkl++ +l +l++q+a+l ++G ev++vsSGav aG + + lp     +a +Q+
  lcl|NCBI__GCF_000020625.1:WP_012506126.1  10 KIVVKVGTNVITNADGKLNLDILDQLTTQIARLCNQGIEVLLVSSGAVGAGRSIITLPVGLPPVARRQV 78 
                                               8******************************************************************** PP

                                 TIGR01027  71 laaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvavee 139
                                               l++ GQ +L+++y +lf+++g ++aQiL t++d+++r++ylN r+ +++l+e  v+p++NEND+v+v+e
  lcl|NCBI__GCF_000020625.1:WP_012506126.1  79 LSSTGQIKLINTYADLFARHGVTTAQILVTKSDFRDRQHYLNMRTCFSSLIEQSVIPVINENDAVSVTE 147
                                               ********************************************************************* PP

                                 TIGR01027 140 ikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTG 208
                                               + f DND+Ls l+a++++ d+ ++l+ vdgL+d    ++ + ++i++++  ++ ++++   + s++G G
  lcl|NCBI__GCF_000020625.1:WP_012506126.1 148 LMFTDNDELSGLIASMMQVDAHIILSHVDGLFDLSK-KKDNPEVIPQIDPEDTRFHKFIQPGKSEFGRG 215
                                               *********************************887.5556789****99999999988888899**** PP

                                 TIGR01027 209 GmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaas.eakGkii 276
                                               Gm tK + a+  +  g+ v ia+g++p  + d++++++vgt+f akk   + rk+w+++ +  +kG+++
  lcl|NCBI__GCF_000020625.1:WP_012506126.1 216 GMLTKCHIARKLAGFGISVHIANGRTPGILYDIVSGKSVGTKFLAKKP-THGRKRWLAHSEgMEKGAVT 283
                                               *********************************************966.789999**99873579**** PP

                                 TIGR01027 277 vdegaeealle..kgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkse 341
                                               +++gae+al++  + +sLlp+g+ +v+g F +g++++i++e+g++ig g+++ysse+ +++ g+  e
  lcl|NCBI__GCF_000020625.1:WP_012506126.1 284 INAGAEKALRSptEANSLLPVGIESVKGAFYKGDIIKICTENGEIIGYGMARYSSEKTRELLGKTGE 350
                                               *********98335678*******************************************9998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (363 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.55
//
[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