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

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.19059.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: 00:00:00.01
# Mc/sec: 9.15
//
[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