Alignments for a candidate for argG in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Desulfotomaculum ruminis DSM 2154

Align argininosuccinate synthase (EC 6.3.4.5) (characterized)
to candidate WP_013840425.1 DESRU_RS01840 argininosuccinate synthase

Query= BRENDA::A4I066
         (418 letters)



>NCBI__GCF_000215085.1:WP_013840425.1
          Length = 401

 Score =  520 bits (1339), Expect = e-152
 Identities = 261/399 (65%), Positives = 315/399 (78%), Gaps = 3/399 (0%)

Query: 14  PRVVLAYSGGLDTSVIIPWLKENYDYEVIACCANVGQGAGEIDGLEEKAKKSGASKLYLL 73
           P+VVLAYSGGLDTSVII WLKENY YEVIA  A++GQG  E+  LEEKA +SGASK+Y+ 
Sbjct: 2   PKVVLAYSGGLDTSVIIAWLKENYGYEVIAMTADLGQGE-ELAPLEEKAIQSGASKIYIE 60

Query: 74  DLREEYVTDYIFPTLKAGATYEGKYMLGTSHARPLIAKHLVEVAHKEGAVAICHGATGKG 133
           DLR+E+V +Y+FPTLKAGA YEGKY+LGTS ARPLIAK LVE+A KEGAVA+ HGATGKG
Sbjct: 61  DLRKEFVEEYVFPTLKAGAVYEGKYLLGTSFARPLIAKKLVEIAEKEGAVAVAHGATGKG 120

Query: 134 NDQVRFELAVMALDPSLKCVAPWREWNIKSREDAIDYAEAHGVPVPCTKSDLYSRDRNLW 193
           NDQVRFEL V AL P LK +APWREW+I+SREDAIDYAEA G+PVP TK  +YSRDRN+W
Sbjct: 121 NDQVRFELGVKALAPHLKVIAPWREWDIRSREDAIDYAEARGIPVPVTKKSIYSRDRNIW 180

Query: 194 HISHEGMDLEDPANEPAYARLLRLCNTVEKAPDEAEYVTVQFEKGIPVAVNGRKMSSVEL 253
           HISHEG +LE PAN PA   +L L    EKAP++  YV + FE+GIPVA+NG K  SV L
Sbjct: 181 HISHEGGELESPAN-PASYDMLMLTVPPEKAPEQPTYVEIGFEQGIPVALNGEKTDSVSL 239

Query: 254 VEELNALGGKHAIGIEDIVEDRLVGMKSRGVYETPAGTILYKALDMLESLCLDRDTQSFK 313
           +E+LN +GG + IGI D+VE+RLVGMKSRGVYETP G IL  A   +E L LDR T  +K
Sbjct: 240 LEKLNEIGGANGIGIVDMVENRLVGMKSRGVYETPGGAILVYAHREMELLTLDRATLHYK 299

Query: 314 RQSAVRFSELVYDGKWFTPLRESMSAMFDQMAETVTGEATLKLYKGNLVPAGAQSPYSLY 373
            Q A+R++ELVYDG WF+PLRE++ A  D    TVTG   LKLYKGN++PAG  SPYSLY
Sbjct: 300 EQMALRYAELVYDGVWFSPLREALDAFVDSTQRTVTGTVKLKLYKGNIIPAGVTSPYSLY 359

Query: 374 NKNIASFGDSQHLYNHHDAEGFIRLFGLPLRVRSMMKAK 412
           ++ +++F   + +YN  DAEGFI LFGLPL+VR++M+ K
Sbjct: 360 DEELSTFSRDE-VYNQADAEGFINLFGLPLKVRALMEKK 397


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: 526
Number of extensions: 17
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: 401
Length adjustment: 31
Effective length of query: 387
Effective length of database: 370
Effective search space:   143190
Effective search space used:   143190
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 WP_013840425.1 DESRU_RS01840 (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.21612.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-160  519.6   0.0   4.1e-160  519.3   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013840425.1  DESRU_RS01840 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013840425.1  DESRU_RS01840 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.3   0.0  4.1e-160  4.1e-160       1     388 [.       3     390 ..       3     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 519.3 bits;  conditional E-value: 4.1e-160
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               kvvlaysGGlDtsv++++l+e+ g+evia+t+d+Gq+ e+l+  eeka++ Ga k y+ D r+efv++y
  lcl|NCBI__GCF_000215085.1:WP_013840425.1   3 KVVLAYSGGLDTSVIIAWLKENyGYEVIAMTADLGQG-EELAPLEEKAIQSGASKIYIEDLRKEFVEEY 70 
                                               8***********************************9.9****************************** PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                               +f++++a+avyegkYll+t+ aRpliakklve+a+kega avahG+tgKGnDqvRFel +++l+p+lkv
  lcl|NCBI__GCF_000215085.1:WP_013840425.1  71 VFPTLKAGAVYEGKYLLGTSFARPLIAKKLVEIAEKEGAVAVAHGATGKGNDQVRFELGVKALAPHLKV 139
                                               ********************************************************************* PP

                                 TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpi 205
                                               iaP+re+++  Re+ i+ya+++Gi+vpv+k++ ys D+n++++s+E+geLE p      d+ +l++ p 
  lcl|NCBI__GCF_000215085.1:WP_013840425.1 140 IAPWREWDIRsREDAIDYAEARGIPVPVTKKSIYSRDRNIWHISHEGGELESPANPASYDMLMLTV-PP 207
                                               ********988*******************************************************.66 PP

                                 TIGR00032 206 ektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapal 274
                                               ek +++p +vei+Fe+G+Pvalnge+ ++v l++k+nei+g++G+G +D+vE+R++g+KsR++YE+p+ 
  lcl|NCBI__GCF_000215085.1:WP_013840425.1 208 EKAPEQPTYVEIGFEQGIPVALNGEKTDSVSLLEKLNEIGGANGIGIVDMVENRLVGMKSRGVYETPGG 276
                                               7777***************************************************************** PP

                                 TIGR00032 275 llLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343
                                               ++L+ Ah+++e l+l++ +l++ke +  +y+el+Y G+wf+pl+ealda+++ tq+ vtGtv++kl+kG
  lcl|NCBI__GCF_000215085.1:WP_013840425.1 277 AILVYAHREMELLTLDRATLHYKEQMALRYAELVYDGVWFSPLREALDAFVDSTQRTVTGTVKLKLYKG 345
                                               ********************************************************************* PP

                                 TIGR00032 344 naivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikv 388
                                               n i +g +s+yslYdeel++f +d+ ++q da+Gfi++ gl+ kv
  lcl|NCBI__GCF_000215085.1:WP_013840425.1 346 NIIPAGVTSPYSLYDEELSTFSRDEVYNQADAEGFINLFGLPLKV 390
                                               *****************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (401 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.64
//
[ok]

This GapMind analysis is from Apr 10 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