Alignments for a candidate for argG in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Burkholderia phytofirmans PsJN

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate BPHYT_RS15920 BPHYT_RS15920 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__BFirm:BPHYT_RS15920
          Length = 408

 Score =  489 bits (1258), Expect = e-143
 Identities = 239/401 (59%), Positives = 304/401 (75%), Gaps = 6/401 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASK--AIAL 59
           K+VLAYSGGLDTS+ILKWL++ Y AEV+ FTADIGQGEE+E AR+KAL+ G  +      
Sbjct: 6   KVVLAYSGGLDTSVILKWLQDNYDAEVVTFTADIGQGEELEPARKKALQLGIKQDNIFIE 65

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           DL+EEFVRDFVFPM RA  +YEG YLLGTSIARPLIAK  + IA   GA+A++HGATGKG
Sbjct: 66  DLREEFVRDFVFPMFRANTIYEGEYLLGTSIARPLIAKRQIEIARATGAQAVSHGATGKG 125

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK---PYSMDA 176
           NDQVRFEL  YAL+P IKVIAPWREW    R++++AYAE  GIP+ +  ++   PYSMDA
Sbjct: 126 NDQVRFELGYYALEPGIKVIAPWREWDLLSREKLLAYAEKAGIPIEMKHKQGGAPYSMDA 185

Query: 177 NLLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPA 236
           NLLHIS+EG  LEDP AE    M+R T  PE+APD  EY+++E+  GDPVA+NG+RLS A
Sbjct: 186 NLLHISFEGRHLEDPKAEAEADMWRWTVSPEQAPDQAEYIDIEYEHGDPVAINGKRLSAA 245

Query: 237 ALLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLH 296
            +L  LN +GG+HG+GR+D+VENR+VGMKSRG YETPGGTI+  A R +ES+TLDREV H
Sbjct: 246 EMLTELNRLGGKHGIGRLDLVENRYVGMKSRGCYETPGGTIMLKAHRGIESITLDREVAH 305

Query: 297 QRDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKS 356
            +D L  +YA L+Y G+W++PER A+Q   DH    V G  R+KLYKG+V VV R + ++
Sbjct: 306 LKDDLMARYASLIYNGYWWSPERRAIQVLIDHTQEKVNGWVRVKLYKGSVSVVARDSKET 365

Query: 357 LYRQDLVSFDEAGG-YDQKDAEGFIKIQALRLRVRALVERE 396
           L+ + + +FD+ GG Y+Q DA GFIK+ ALR+R+     R+
Sbjct: 366 LFDKTIATFDDDGGAYNQADAGGFIKLNALRMRIAENARRQ 406


Lambda     K      H
   0.319    0.137    0.402 

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: 538
Number of extensions: 18
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: 400
Length of database: 408
Length adjustment: 31
Effective length of query: 369
Effective length of database: 377
Effective search space:   139113
Effective search space used:   139113
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS15920 BPHYT_RS15920 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.8657.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.7e-147  477.1   0.0   3.1e-147  476.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS15920  BPHYT_RS15920 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS15920  BPHYT_RS15920 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.9   0.0  3.1e-147  3.1e-147       1     390 [.       6     401 ..       6     405 .. 0.96

  Alignments for each domain:
  == domain 1  score: 476.9 bits;  conditional E-value: 3.1e-147
                                TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaek..ayviDareefvkd 67 
                                              kvvlaysGGlDtsv+lk+l+++  aev+++t+d+Gq+ e+l+ +++kal+lG ++    + D reefv+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS15920   6 KVVLAYSGGLDTSVILKWLQDNyDAEVVTFTADIGQG-EELEPARKKALQLGIKQdnIFIEDLREEFVRD 74 
                                              8*********************99************9.9*************875114556********* PP

                                TIGR00032  68 ylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                              ++f+  +an++yeg+Yll+t++aRpliak+++e+a+  ga+av+hG+tgKGnDqvRFel  ++l+p +kv
  lcl|FitnessBrowser__BFirm:BPHYT_RS15920  75 FVFPMFRANTIYEGEYLLGTSIARPLIAKRQIEIARATGAQAVSHGATGKGNDQVRFELGYYALEPGIKV 144
                                              ********************************************************************** PP

                                TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvekek...aysiDenllgrsiEageLEdpsteppediyelvkd 203
                                              iaP+re++l  Re++++ya++ Gi++++++++   +ys+D nll++s E+ +LEdp++e   d+++++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS15920 145 IAPWREWDLLsREKLLAYAEKAGIPIEMKHKQggaPYSMDANLLHISFEGRHLEDPKAEAEADMWRWTVS 214
                                              ********987****************998644449*********************************9 PP

                                TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapa 273
                                              p++++ d++e+++ie+e+G Pva+ng++l++ e++ ++n+++gkhG+Gr+D vE+R++g+KsR++YE+p+
  lcl|FitnessBrowser__BFirm:BPHYT_RS15920 215 PEQAP-DQAEYIDIEYEHGDPVAINGKRLSAAEMLTELNRLGGKHGIGRLDLVENRYVGMKSRGCYETPG 283
                                              98888.**************************************************************** PP

                                TIGR00032 274 lllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343
                                               ++++kAh+ +e+ +l+++v+++k+    +y+ liY+G+w++p++ a++ li++tqe+v+G+vrvkl+kG
  lcl|FitnessBrowser__BFirm:BPHYT_RS15920 284 GTIMLKAHRGIESITLDREVAHLKDDLMARYASLIYNGYWWSPERRAIQVLIDHTQEKVNGWVRVKLYKG 353
                                              ********************************************************************** PP

                                TIGR00032 344 naivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyr 390
                                              ++ v++r+s+++l+d+++++f+    +++q da Gfik+++l++++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS15920 354 SVSVVARDSKETLFDKTIATFDDdGGAYNQADAGGFIKLNALRMRIAE 401
                                              **********************8446799*************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (408 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: 6.97
//
[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