Alignments for a candidate for argG in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Stenotrophomonas chelatiphaga DSM 21508

Align arginosuccinate synthetase (EC 6.3.4.5) (characterized)
to candidate WP_057687253.1 ABB28_RS15385 argininosuccinate synthase

Query= reanno::Dyella79:N515DRAFT_3766
         (398 letters)



>NCBI__GCF_001431535.1:WP_057687253.1
          Length = 397

 Score =  680 bits (1755), Expect = 0.0
 Identities = 327/395 (82%), Positives = 363/395 (91%)

Query: 2   SKDIVLAFSGGLDTSFCVPYLKERGWNVHTVFADTGGVDAEERAYIEARAQELGVASHVT 61
           +KD+VLAFSGGLDTSFCVPYL+ERG+NVHTVFADTGGVD EER +IE RA ELGV SHVT
Sbjct: 3   NKDVVLAFSGGLDTSFCVPYLQERGYNVHTVFADTGGVDDEERDFIEKRAAELGVTSHVT 62

Query: 62  VDGGPAIWNGFVKPFVWAGEGYQGQYPLLVSDRYLIVDAAIQRCAELGTRAIAHGCTGMG 121
           VDGGPAIW GFVKPFVWAGEGYQGQYPLLVSDRYLIVDAA++R AELGT  IAHGCTGMG
Sbjct: 63  VDGGPAIWEGFVKPFVWAGEGYQGQYPLLVSDRYLIVDAALKRAAELGTNIIAHGCTGMG 122

Query: 122 NDQVRFDLAVKALGDYEIVAPIREIQKEHTQTRAYEQAYLEERGFPVRAKQKSYTINENL 181
           NDQVRFDLAVKALGDY+I+APIREIQKEHTQTRAYEQ YLEERGF VRAKQ++YTINENL
Sbjct: 123 NDQVRFDLAVKALGDYQIIAPIREIQKEHTQTRAYEQKYLEERGFGVRAKQQAYTINENL 182

Query: 182 LGVTLSGGEIDLWKAPGEGARGWCKPRAEWPSEKLSVTLGFEHGEAVSLNGEKLPGAKIL 241
           LG+T+SGGEID W+APGEGARGWC PR+EWP + L+VTL F  G AV L+G+ LPG KIL
Sbjct: 183 LGLTMSGGEIDRWEAPGEGARGWCAPRSEWPEQALTVTLKFVDGVAVELDGKALPGEKIL 242

Query: 242 ARLNELFAPYGVGRGMYTGDTTIGLKGRIVYEAPGLISLLAAHRALEEAVLTKQQNRFKP 301
           A LN+LFAPYGVGRG+YTGDT IGLKGRIV+EAPGL+SLLAAHRALE+AVLTKQQNRFKP
Sbjct: 243 ATLNKLFAPYGVGRGVYTGDTVIGLKGRIVFEAPGLVSLLAAHRALEDAVLTKQQNRFKP 302

Query: 302 EIARKWVEVVYEGFFHDPVKTDLEAFLASSQQQVNGDVVLETSGAQVTAVEVRSPHILNA 361
           ++ARKWVE+VYEGF+HDP+KTD+EAFL SSQ +VNG+VVLET G +V AV VRSPH+LN 
Sbjct: 303 DVARKWVELVYEGFYHDPLKTDIEAFLKSSQAKVNGEVVLETRGGRVDAVAVRSPHLLNT 362

Query: 362 KGATYAQSADWGVAEAEGFIKLFGMSSTLWAEVNR 396
           KGATYAQSADWGV EAEGFIKLFGMSSTL+A+VNR
Sbjct: 363 KGATYAQSADWGVEEAEGFIKLFGMSSTLYAQVNR 397


Lambda     K      H
   0.317    0.135    0.408 

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: 652
Number of extensions: 24
Number of successful extensions: 1
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: 398
Length of database: 397
Length adjustment: 31
Effective length of query: 367
Effective length of database: 366
Effective search space:   134322
Effective search space used:   134322
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_057687253.1 ABB28_RS15385 (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.30141.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.3e-85  271.8   0.0    7.2e-85  271.6   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057687253.1  ABB28_RS15385 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687253.1  ABB28_RS15385 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.6   0.0   7.2e-85   7.2e-85       2     392 ..       6     395 ..       5     397 .] 0.96

  Alignments for each domain:
  == domain 1  score: 271.6 bits;  conditional E-value: 7.2e-85
                                 TIGR00032   2 vvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdyl 69 
                                               vvla+sGGlDts ++++l+e+g++v +v +d G   +e+ d ie++a +lG++ ++++D+   + + ++
  lcl|NCBI__GCF_001431535.1:WP_057687253.1   6 VVLAFSGGLDTSFCVPYLQERGYNVHTVFADTGGVdDEERDFIEKRAAELGVTSHVTVDGGPAIWEGFV 74 
                                               9********************************9878999***************************** PP

                                 TIGR00032  70 faaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkvi 138
                                                + + a+  y+g+Y+l  +  R li  + ++ a + g++++ahGctg GnDqvRF+l ++    d ++i
  lcl|NCBI__GCF_001431535.1:WP_057687253.1  75 KPFVWAGEGYQGQYPLLVS-DRYLIVDAALKRAAELGTNIIAHGCTGMGNDQVRFDLAVK-ALGDYQII 141
                                               ****************987.7***************************************.5689**** PP

                                 TIGR00032 139 aPvreleli....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkd 203
                                               aP+re++      R+ e +y++e+G+ v+++ ++ay i+enllg ++ +ge++  + +p e +  + + 
  lcl|NCBI__GCF_001431535.1:WP_057687253.1 142 APIREIQKEhtqtRAYEQKYLEERGFGVRAK-QQAYTINENLLGLTMSGGEID-RWEAPGEGARGWCA- 207
                                               *****99766788****************98.69*****************95.6889*********9. PP

                                 TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272
                                               p  + ++++ +v+++F +Gv v l+g+ l   +++ ++n++    GvGr     d +iglK R ++Eap
  lcl|NCBI__GCF_001431535.1:WP_057687253.1 208 PRSEWPEQALTVTLKFVDGVAVELDGKALPGEKILATLNKLFAPYGVGRGVYTGDTVIGLKGRIVFEAP 276
                                               999999*************************************************************** PP

                                 TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklf 341
                                               +l+ L+ Ah++Le+ vltk++ +fk  v +k+ el+Y+G+++dpl+ +++a++k +q +v+G+v ++ +
  lcl|NCBI__GCF_001431535.1:WP_057687253.1 277 GLVSLLAAHRALEDAVLTKQQNRFKPDVARKWVELVYEGFYHDPLKTDIEAFLKSSQAKVNGEVVLETR 345
                                               ********************************************************************* PP

                                 TIGR00032 342 kGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvyrek 392
                                                G +  ++ +s+++l + + +++ + +    ++a+Gfik+ g++ + y+++
  lcl|NCBI__GCF_001431535.1:WP_057687253.1 346 GGRVDAVAVRSPHLL-NTKGATYAQSADWGVEEAEGFIKLFGMSSTLYAQV 395
                                               ********9999876.678899**9*******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (397 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.25
//
[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