Aligments for a candidate for argG in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Aligments for a candidate for argG in Shewanella loihica PV-4

Align argininosuccinate synthase (EC 6.3.4.5) (characterized)
to candidate 5207683 Shew_0205 argininosuccinate synthase (RefSeq)

Query= BRENDA::A4I066
         (418 letters)



>lcl|FitnessBrowser__PV4:5207683 Shew_0205 argininosuccinate
           synthase (RefSeq)
          Length = 407

 Score =  418 bits (1075), Expect = e-121
 Identities = 209/395 (52%), Positives = 270/395 (68%), Gaps = 3/395 (0%)

Query: 15  RVVLAYSGGLDTSVIIPWLKENYDY-EVIACCANVGQGAGEIDGLEEKAKKSGASKLYLL 73
           +VVLAYSGGLDTS IIPWLKE YD  E++A CA+VGQG  E++GL EKA  SGAS+ Y++
Sbjct: 12  KVVLAYSGGLDTSAIIPWLKETYDNCEIVAFCADVGQGEAELEGLHEKAIASGASECYIV 71

Query: 74  DLREEYVTDYIFPTLKAGATYEGKYMLGTSHARPLIAKHLVEVAHKEGAVAICHGATGKG 133
           DL+EE V DYI+PT+  GA YEG Y+LGTS ARP+IAK  VEVA K GA A+CHG TGKG
Sbjct: 72  DLKEELVADYIYPTIATGAIYEGTYLLGTSMARPIIAKAQVEVARKVGADAVCHGCTGKG 131

Query: 134 NDQVRFELAVMALDPSLKCVAPWREWNIKSREDAIDYAEAHGVPVPCTKSDLYSRDRNLW 193
           NDQVRFE    AL P L  +APWREW++ SRED +DY     +    + + +YSRD N W
Sbjct: 132 NDQVRFEGCFAALAPDLTVIAPWREWSMVSREDLLDYLAERNIKTTASATKIYSRDANAW 191

Query: 194 HISHEGMDLEDPANEPAYARLLRLCNTVEKAPDEAEYVTVQFEKGIPVAVNGRKMSSVEL 253
           HISHEG +LEDP NEP+   +  +    E APDE EYV+V+ E G    VNG+  +    
Sbjct: 192 HISHEGGELEDPWNEPS-KEVWTMTVAPEDAPDEPEYVSVEMEAGRITKVNGQSYTPYGA 250

Query: 254 VEELNALGGKHAIGIEDIVEDRLVGMKSRGVYETPAGTILYKALDMLESLCLDRDTQSFK 313
           +  LN + G H +G  DI E+RLVGMKSRG YETP GT+++ AL  +E L LD+ ++ ++
Sbjct: 251 LMALNEIAGAHGVGRIDITENRLVGMKSRGCYETPGGTVMFAALRAIEELVLDKTSREWR 310

Query: 314 RQSAVRFSELVYDGKWFTPLRESMSAMFDQMAETVTGEATLKLYKGNLVPAGAQSPYSLY 373
            Q   + + LVYDG+WFTPL ES+      +A  + GE  LKLYKG       +SP SLY
Sbjct: 311 EQVGAKMAHLVYDGRWFTPLCESLLGASQPLANLLNGEVVLKLYKGQAQAVKKRSPNSLY 370

Query: 374 NKNIASFGDSQHLYNHHDAEGFIRLFGLPLRVRSM 408
           ++  A+FG+ + +YN  DAEGFIRL+ L  R+R++
Sbjct: 371 SEEFATFGEDE-VYNQKDAEGFIRLYSLASRIRAL 404


Lambda     K      H
   0.317    0.134    0.397 

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: 479
Number of extensions: 16
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: 418
Length of database: 407
Length adjustment: 31
Effective length of query: 387
Effective length of database: 376
Effective search space:   145512
Effective search space used:   145512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 5207683 Shew_0205 (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.23437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   9.1e-142  458.9   0.0     1e-141  458.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207683  Shew_0205 argininosuccinate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207683  Shew_0205 argininosuccinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.7   0.0    1e-141    1e-141       1     388 [.      12     401 ..      12     407 .] 0.98

  Alignments for each domain:
  == domain 1  score: 458.7 bits;  conditional E-value: 1e-141
                        TIGR00032   1 kvvlaysGGlDtsvalklleek..gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiqan 76 
                                      kvvlaysGGlDts+++++l+e   ++e++a+++dvGq+e++l+  +eka++ Ga + y++D +ee+v+dy+ ++i ++
  lcl|FitnessBrowser__PV4:5207683  12 KVVLAYSGGLDTSAIIPWLKETydNCEIVAFCADVGQGEAELEGLHEKAIASGASECYIVDLKEELVADYIYPTIATG 89 
                                      8********************98788**************************************************** PP

                        TIGR00032  77 avyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Reeeie 153
                                      a+yeg+Yll+t++aRp+iak++veva+k ga+av hGctgKGnDqvRFe  + +l+pdl viaP+re+ ++ Re++++
  lcl|FitnessBrowser__PV4:5207683  90 AIYEGTYLLGTSMARPIIAKAQVEVARKVGADAVCHGCTGKGNDQVRFEGCFAALAPDLTVIAPWREWSMVsREDLLD 167
                                      *********************************************************************998****** PP

                        TIGR00032 154 yaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvPvalnges 231
                                      y+ae+ i++ ++  k ys D n +++s+E+geLEdp+ ep ++++++++ p++++ depe+v +e e G   ++ng+s
  lcl|FitnessBrowser__PV4:5207683 168 YLAERNIKTTASATKIYSRDANAWHISHEGGELEDPWNEPSKEVWTMTVAPEDAP-DEPEYVSVEMEAGRITKVNGQS 244
                                      *************************************************887777.********************** PP

                        TIGR00032 232 lepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliY 309
                                      ++p   + ++neiag+hGvGriDi E+R++g+KsR++YE+p+ +++  A +++e+lvl+k  +e++e v+ k+++l+Y
  lcl|FitnessBrowser__PV4:5207683 245 YTPYGALMALNEIAGAHGVGRIDITENRLVGMKSRGCYETPGGTVMFAALRAIEELVLDKTSREWREQVGAKMAHLVY 322
                                      ****************************************************************************** PP

                        TIGR00032 310 kGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqik 387
                                       G+wf pl+e l  + +  ++ ++G+v +kl+kG+a  + ++s++slY+ee ++f +d+ ++qkda+Gfi++++l  +
  lcl|FitnessBrowser__PV4:5207683 323 DGRWFTPLCESLLGASQPLANLLNGEVVLKLYKGQAQAVKKRSPNSLYSEEFATFGEDEVYNQKDAEGFIRLYSLASR 400
                                      *************************************************************************99876 PP

                        TIGR00032 388 v 388
                                      +
  lcl|FitnessBrowser__PV4:5207683 401 I 401
                                      5 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.51
//
[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