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.2483381.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.00
//
[ok]

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

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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:

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:

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:

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:

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