Alignments for a candidate for argG in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Synechococcus elongatus PCC 7942

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate Synpcc7942_0009 Synpcc7942_0009 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__SynE:Synpcc7942_0009
          Length = 400

 Score =  376 bits (965), Expect = e-109
 Identities = 187/395 (47%), Positives = 265/395 (67%), Gaps = 2/395 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAE-VIAFTADIGQGEEVEEAREKALRTGASKAIALD 60
           ++VLAYSGG+DTS+ + +LK+ +  E VI   AD+GQG+E+   R+KAL +GA +++ +D
Sbjct: 6   RVVLAYSGGVDTSVCIPYLKQEWGVEEVITLAADLGQGDELGPIRQKALDSGAVESLVID 65

Query: 61  LKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGN 120
              EFVRD+ FP ++A ++YEG Y L T++ARPLIAK LV  A + GA+A+AHG TGKGN
Sbjct: 66  ATAEFVRDYAFPAIQANSLYEGRYPLSTALARPLIAKLLVEAAAKYGADAVAHGCTGKGN 125

Query: 121 DQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLH 180
           DQVRF+++  AL PD+KV+AP REW    R+E IAY E  GIP PV +  PYS+D NLL 
Sbjct: 126 DQVRFDVSIAALNPDLKVLAPAREWGMS-REETIAYGERFGIPAPVKKSSPYSIDRNLLG 184

Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240
            S E G LEDP  EP + ++ +T+     PD P Y+E+ F +G PV +NG+ L+P AL+Q
Sbjct: 185 RSIEAGPLEDPLHEPLEEVYALTKAIANTPDEPAYIELGFDQGLPVTLNGQALAPVALIQ 244

Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300
           +LN I G HG+GR+D++ENR VG+KSR +YETP   +L  A + +ESL L  +V   +  
Sbjct: 245 QLNAIAGEHGIGRIDMIENRLVGIKSREIYETPALLVLIQAHQDLESLVLTADVSQYKRG 304

Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360
           +   ++ LVY G WY+P + AL A+     + VTG  RL+L+KGN  VVGR + +SLY  
Sbjct: 305 IENSWSNLVYNGLWYSPLKAALDAFIQQTQQRVTGTVRLRLFKGNATVVGRSSEQSLYSP 364

Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALRLRVRALVER 395
           D+ ++     +D K AEGFI +  +  R+ +   R
Sbjct: 365 DMATYGAEDRFDHKAAEGFIYVWGMPTRIWSQTHR 399


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: 411
Number of extensions: 12
Number of successful extensions: 3
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 Synpcc7942_0009 Synpcc7942_0009 (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.24274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-172  560.3   0.0   1.7e-172  560.1   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0009  Synpcc7942_0009 argininosuccinat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0009  Synpcc7942_0009 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.1   0.0  1.7e-172  1.7e-172       1     392 [.       6     397 ..       6     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 560.1 bits;  conditional E-value: 1.7e-172
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.ga.eviavtvdvGqpeedldaieekalklGaekayviDareefvkd 67 
                                               +vvlaysGG+Dtsv++++l+++ g+ evi++++d+Gq+ ++l  i++kal  Ga++++viDa +efv+d
  lcl|FitnessBrowser__SynE:Synpcc7942_0009   6 RVVLAYSGGVDTSVCIPYLKQEwGVeEVITLAADLGQG-DELGPIRQKALDSGAVESLVIDATAEFVRD 73 
                                               69**********************999**********9.****************************** PP

                                 TIGR00032  68 ylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlk 136
                                               y+f+aiqan++yeg+Y+lstaLaRpliak lve+a k+ga+avahGctgKGnDqvRF++si +lnpdlk
  lcl|FitnessBrowser__SynE:Synpcc7942_0009  74 YAFPAIQANSLYEGRYPLSTALARPLIAKLLVEAAAKYGADAVAHGCTGKGNDQVRFDVSIAALNPDLK 142
                                               ********************************************************************* PP

                                 TIGR00032 137 viaPvreleliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpi 205
                                               v+aP+re+ ++Ree+i+y ++ Gi+ pv+k+++ysiD+nllgrsiEag LEdp  ep e++y+l+k +i
  lcl|FitnessBrowser__SynE:Synpcc7942_0009 143 VLAPAREWGMSREETIAYGERFGIPAPVKKSSPYSIDRNLLGRSIEAGPLEDPLHEPLEEVYALTK-AI 210
                                               ******************************************************************.99 PP

                                 TIGR00032 206 ektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapal 274
                                               ++t+dep ++e++F++G+Pv+lng+ l pv li+++n iag+hG+GriD++E+R++g+KsReiYE+pal
  lcl|FitnessBrowser__SynE:Synpcc7942_0009 211 ANTPDEPAYIELGFDQGLPVTLNGQALAPVALIQQLNAIAGEHGIGRIDMIENRLVGIKSREIYETPAL 279
                                               9999***************************************************************** PP

                                 TIGR00032 275 llLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343
                                               l+Li+Ah+dLe+lvlt+dv ++k+ +e+++s+l+Y+Glw++pl+ alda+i++tq+rvtGtvr++lfkG
  lcl|FitnessBrowser__SynE:Synpcc7942_0009 280 LVLIQAHQDLESLVLTADVSQYKRGIENSWSNLVYNGLWYSPLKAALDAFIQQTQQRVTGTVRLRLFKG 348
                                               ********************************************************************* PP

                                 TIGR00032 344 naivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvyrek 392
                                               na+v+gr+se+slY+++++++  +++fd+k+a+Gfi+++g+++++++++
  lcl|FitnessBrowser__SynE:Synpcc7942_0009 349 NATVVGRSSEQSLYSPDMATYGAEDRFDHKAAEGFIYVWGMPTRIWSQT 397
                                               ********************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (400 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: 00:00:00.01
# Mc/sec: 10.66
//
[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