Alignments for a candidate for proB in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Phaeobacter inhibens BS107

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate GFF1532 PGA1_c15510 glutamate 5-kinase ProB

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



>FitnessBrowser__Phaeo:GFF1532
          Length = 368

 Score =  302 bits (774), Expect = 8e-87
 Identities = 180/363 (49%), Positives = 238/363 (65%), Gaps = 10/363 (2%)

Query: 11  RLVVKIGSALLVD-PEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGARRLKLAK 69
           R+VVKIGSALLVD   GA+R DWL  +AAD+A     G+ + +VSSG+IALG R L LA 
Sbjct: 9   RIVVKIGSALLVDRTSGALRADWLRALAADVAWLKSMGKDVILVSSGSIALGRRVLGLA- 67

Query: 70  GGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNAAATLGR 129
                LE +QAAAA GQI L+  + E LA + +T AQ+LVTL+D  DRRRYLN+ ATL  
Sbjct: 68  AQELPLEQSQAAAAVGQIRLAGAYEEALAPHEITTAQVLVTLEDSADRRRYLNSRATLET 127

Query: 130 LLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDRNPAL-P 188
           L+ LGVVP++NEND++AT EIR+GDNDRLAA+VA    A  ++LLSD+DG Y  NP L P
Sbjct: 128 LIGLGVVPIVNENDTIATDEIRYGDNDRLAAQVAVTVGADALILLSDVDGFYTANPVLDP 187

Query: 189 GAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANGRVDRPL 248
            A    +++RI   +E MA  G  SG+  GGM++K+ AA++A +AG ++AI  G  + PL
Sbjct: 188 TARRYDIIDRITPEIEAMAGDG-VSGLSKGGMITKLLAAKMATAAGCAMAITEGSPNNPL 246

Query: 249 SA---DARHTVFLPEKRTR-ARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIGATAI 304
                 A  T F  +   + ARK W+A   T +G + VD GAA+AL  G+SLL  G   I
Sbjct: 247 KLLENGAPSTWFTAQDDPQVARKRWIAAMKT-RGVVAVDEGAARALGSGKSLLPAGIRHI 305

Query: 305 RGMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVHRNH 363
            G F RGD + I GP+G  + +GLS Y A +A AI G +S +   ILGYA R+ ++HR+ 
Sbjct: 306 EGDFGRGDPLAILGPDGRKLGQGLSRYTAEEASAIKGCQSTEIEAILGYAGRAAVIHRDD 365

Query: 364 MAL 366
           MAL
Sbjct: 366 MAL 368


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: 372
Number of extensions: 27
Number of successful extensions: 7
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: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
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: 49 (23.5 bits)

Align candidate GFF1532 PGA1_c15510 (glutamate 5-kinase ProB)
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.20705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.2e-117  379.1   0.1   1.3e-117  378.9   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1532  PGA1_c15510 glutamate 5-kinase P


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1532  PGA1_c15510 glutamate 5-kinase ProB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.9   0.1  1.3e-117  1.3e-117       1     362 [.       8     367 ..       8     368 .] 0.98

  Alignments for each domain:
  == domain 1  score: 378.9 bits;  conditional E-value: 1.3e-117
                          TIGR01027   1 kriVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVG 75 
                                        +riVvK+Gs++L++ ++  l++  l++l+++va lk++G++v++vsSG++a G + Lgl  ++  l++ Qa+aaVG
  lcl|FitnessBrowser__Phaeo:GFF1532   8 QRIVVKIGSALLVDRTSGaLRADWLRALAADVAWLKSMGKDVILVSSGSIALGRRVLGLAAQELPLEQSQAAAAVG 83 
                                        69***********987766********************************************************* PP

                          TIGR01027  76 QgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsal 151
                                        Q rL  +ye++++ +++++aQ+L t +d ++r+rylN r+tle+l+ lgvvpivNENDt+a++ei+ GDND+L+a+
  lcl|FitnessBrowser__Phaeo:GFF1532  84 QIRLAGAYEEALAPHEITTAQVLVTLEDSADRRRYLNSRATLETLIGLGVVPIVNENDTIATDEIRYGDNDRLAAQ 159
                                        **************************************************************************** PP

                          TIGR01027 152 vaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragvev 227
                                        va  v+Ad+L+ll+dvdg y+a+p  +p+A++ + +++i+ e++a+ag++ s +  GGm tKl aa++A++ag  +
  lcl|FitnessBrowser__Phaeo:GFF1532 160 VAVTVGADALILLSDVDGFYTANPVLDPTARRYDIIDRITPEIEAMAGDGVSGLSKGGMITKLLAAKMATAAGCAM 235
                                        **************************************************************************** PP

                          TIGR01027 228 iiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegn 303
                                         i++g+ p++ ++lle+ a  t f+a++    +rk+wi+a+++ +G + vdega++al + gksLlpag+ ++eg+
  lcl|FitnessBrowser__Phaeo:GFF1532 236 AITEGS-PNNPLKLLENGAPSTWFTAQDDPQVARKRWIAAMKT-RGVVAVDEGAARALGS-GKSLLPAGIRHIEGD 308
                                        *****9.79999999999********************98765.5**************9.*************** PP

                          TIGR01027 304 FsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                        F rg+ + il ++g+++g+gl++y++ee + ikg +s+eie++Lgy  ++ v+hrd+++
  lcl|FitnessBrowser__Phaeo:GFF1532 309 FGRGDPLAILGPDGRKLGQGLSRYTAEEASAIKGCQSTEIEAILGYAGRAAVIHRDDMA 367
                                        *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (368 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.83
//
[ok]

This GapMind analysis is from Apr 09 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