GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Shewanella sp. ANA-3

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate 7026770 Shewana3_3902 argininosuccinate synthase (RefSeq)

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__ANA3:7026770
          Length = 407

 Score =  423 bits (1088), Expect = e-123
 Identities = 214/393 (54%), Positives = 274/393 (69%), Gaps = 2/393 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETY-RAEVIAFTADIGQGEE-VEEAREKALRTGASKAIAL 59
           K+VLAYSGGLDTS I+ WLKETY   E+IAF AD+GQGEE +    EKAL +GAS+   +
Sbjct: 12  KVVLAYSGGLDTSAIIPWLKETYDNCEIIAFCADVGQGEEELVGLTEKALASGASECHIV 71

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           DLKEEFV+D+++P M  GA+YEG YLLGTS+ARP+IAK  V +A + GA+A+ HG TGKG
Sbjct: 72  DLKEEFVKDYIYPTMATGAIYEGTYLLGTSMARPIIAKAQVEVARKVGADALCHGCTGKG 131

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLL 179
           NDQVRFE    AL PD+KVIAPWREW+ Q R++++AY     I    +  K YS DAN  
Sbjct: 132 NDQVRFEGCFAALAPDLKVIAPWREWTMQSREDLLAYLAERNIKTSASATKIYSRDANAF 191

Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239
           HIS+EGG LEDPW EP KG++ +T DPE+AP+  EYV +E   G    VNGE L+P A L
Sbjct: 192 HISHEGGELEDPWNEPSKGVWTLTADPEDAPNQAEYVSLEVEHGRVTKVNGEALTPYAAL 251

Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299
            +LN I   HGVGR+DI ENR VGMKSRG YETPGGT+++ A RA+E L LD+     R+
Sbjct: 252 MKLNAIAAPHGVGRIDITENRLVGMKSRGCYETPGGTVMFAALRAIEELVLDKTSRTWRE 311

Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359
            +  + A LVY G W+ P  ++L A  + +A SV G   +KLYKG+   V +++P SLY 
Sbjct: 312 QVGAQMAHLVYDGRWFTPLCKSLLAASESLAESVNGEVVVKLYKGHAIAVKKRSPNSLYS 371

Query: 360 QDLVSFDEAGGYDQKDAEGFIKIQALRLRVRAL 392
           +   +F E   YDQK AEGFI++ +L  R+RAL
Sbjct: 372 EAFATFGEDQVYDQKHAEGFIRLYSLASRIRAL 404


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: 441
Number of extensions: 14
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: 407
Length adjustment: 31
Effective length of query: 369
Effective length of database: 376
Effective search space:   138744
Effective search space used:   138744
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 7026770 Shewana3_3902 (argininosuccinate synthase (RefSeq))
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.1165172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.9e-138  447.4   0.0   3.2e-138  447.2   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026770  Shewana3_3902 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026770  Shewana3_3902 argininosuccinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.2   0.0  3.2e-138  3.2e-138       1     387 [.      12     400 ..      12     407 .] 0.98

  Alignments for each domain:
  == domain 1  score: 447.2 bits;  conditional E-value: 3.2e-138
                         TIGR00032   1 kvvlaysGGlDtsvalklleek..gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiqa 75 
                                       kvvlaysGGlDts+++++l+e   ++e+ia+++dvGq+ee+l    ekal+ Ga +  ++D +eefvkdy+ +++ +
  lcl|FitnessBrowser__ANA3:7026770  12 KVVLAYSGGLDTSAIIPWLKETydNCEIIAFCADVGQGEEELVGLTEKALASGASECHIVDLKEEFVKDYIYPTMAT 88 
                                       8********************98788*************************************************** PP

                         TIGR00032  76 navyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Reee 151
                                       +a+yeg+Yll+t++aRp+iak++veva+k ga+a+ hGctgKGnDqvRFe  + +l+pdlkviaP+re+ +  Re++
  lcl|FitnessBrowser__ANA3:7026770  89 GAIYEGTYLLGTSMARPIIAKAQVEVARKVGADALCHGCTGKGNDQVRFEGCFAALAPDLKVIAPWREWTMQsREDL 165
                                       ***********************************************************************88**** PP

                         TIGR00032 152 ieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvPvaln 228
                                       ++y+ae+ i++ ++  k ys D n +++s+E+geLEdp+ ep + +++l++dp++++ +++e+v +e e+G   ++n
  lcl|FitnessBrowser__ANA3:7026770 166 LAYLAERNIKTSASATKIYSRDANAFHISHEGGELEDPWNEPSKGVWTLTADPEDAP-NQAEYVSLEVEHGRVTKVN 241
                                       ***************************************************999998.999**************** PP

                         TIGR00032 229 geslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekys 305
                                       ge l+p   + k+n ia  hGvGriDi E+R++g+KsR++YE+p+ +++  A +++e+lvl+k  + ++e v+ +++
  lcl|FitnessBrowser__ANA3:7026770 242 GEALTPYAALMKLNAIAAPHGVGRIDITENRLVGMKSRGCYETPGGTVMFAALRAIEELVLDKTSRTWREQVGAQMA 318
                                       ***************************************************************************** PP

                         TIGR00032 306 eliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikir 382
                                       +l+Y G+wf pl++ l a+ +  +e+v+G+v vkl+kG+ai + ++s++slY+e  ++f +d+ +dqk+a+Gfi+++
  lcl|FitnessBrowser__ANA3:7026770 319 HLVYDGRWFTPLCKSLLAASESLAESVNGEVVVKLYKGHAIAVKKRSPNSLYSEAFATFGEDQVYDQKHAEGFIRLY 395
                                       ***************************************************************************** PP

                         TIGR00032 383 glqik 387
                                       +l  +
  lcl|FitnessBrowser__ANA3:7026770 396 SLASR 400
                                       99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (407 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.23
//
[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