Alignments for a candidate for argG in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Mycolicibacterium vanbaalenii PYR-1

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_011780511.1 MVAN_RS16595 argininosuccinate synthase

Query= SwissProt::Q9X2A1
         (409 letters)



>NCBI__GCF_000015305.1:WP_011780511.1
          Length = 400

 Score =  286 bits (732), Expect = 8e-82
 Identities = 164/400 (41%), Positives = 242/400 (60%), Gaps = 18/400 (4%)

Query: 1   MKEKVVLAYSGGLDTSVILKWLC-EKGFDVIAYVANVGQK-DDFVAIKEKALKTGASKVY 58
           M E+V+LAYSGGLDTSV + W+  E G +V+A   ++GQ  +D   ++++AL  GA +  
Sbjct: 1   MSERVILAYSGGLDTSVAISWIGKETGSEVVAVAIDLGQGGEDMEVVRQRALDCGAVEAV 60

Query: 59  VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 118
           V D R EF   Y   A+  NA+Y  RY L +A++RPLI K  V+ A + G   VAHG TG
Sbjct: 61  VVDARDEFAEQYCLPAIKSNALYMDRYPLVSALSRPLIVKHLVDAAREHGGGVVAHGCTG 120

Query: 119 KGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFKGRTDLINYAMEKGIPIKVSKKRPYS 178
           KGNDQVRFE+ +A+L P+LKV++P +D  +      R   I +A E  IPI V+K+ P+S
Sbjct: 121 KGNDQVRFEVGFASLAPDLKVLAPVRDYAWT-----REKAIAFAEENAIPINVTKRSPFS 175

Query: 179 EDENLMHISHEAGKLEDPAHIPDEDVFTWTVSPK---DAPDEETLLEIHFENGIPVKVVN 235
            D+N+   + E G LE   + P +DV+ +T  P     +PDE   + I F+ G+PV +  
Sbjct: 176 IDQNVWGRAVETGFLEHLWNAPTKDVYDYTEDPTLNWSSPDE---VIIGFDKGVPVSI-- 230

Query: 236 LKDGTEKTDPLELFEYLNEVGAKNGVGRLDMVENRFIGIKSRGVYETPGATILWIAHRDL 295
             DG   T  L+  E LN      GVGRLD+VE+R +GIKSR +YE PGA +L  AH +L
Sbjct: 231 --DGKPVT-VLQAIEQLNARAGAQGVGRLDVVEDRLVGIKSREIYEAPGAMVLITAHTEL 287

Query: 296 EGITMDKEVMHLRDMLAPKFAELIYNGFWFSPEMEFLLAAFRKAQENVTGKVTVSIYKGN 355
           E +T+++E+   +     K+ EL+Y+G WFSP    L +     QE+VTG++ + ++ G+
Sbjct: 288 EHVTLERELGRFKRTTDQKWGELVYDGLWFSPLKTALESFVANTQEHVTGEIRLVLHGGH 347

Query: 356 VMPVARYSPYSLYNPELSSMDVEGGFDATDSKGFINIHAL 395
           +    R S  SLY+  L++ D    FD + +KGF+++H L
Sbjct: 348 IAVNGRRSQESLYDFNLATYDEGDTFDQSAAKGFVHVHGL 387


Lambda     K      H
   0.318    0.137    0.400 

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: 415
Number of extensions: 24
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: 409
Length of database: 400
Length adjustment: 31
Effective length of query: 378
Effective length of database: 369
Effective search space:   139482
Effective search space used:   139482
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_011780511.1 MVAN_RS16595 (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.4159437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-149  484.7   0.0   1.5e-149  484.5   0.0    1.0  1  NCBI__GCF_000015305.1:WP_011780511.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015305.1:WP_011780511.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.5   0.0  1.5e-149  1.5e-149       1     389 [.       4     392 ..       4     396 .. 0.99

  Alignments for each domain:
  == domain 1  score: 484.5 bits;  conditional E-value: 1.5e-149
                             TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaa 72 
                                           +v+laysGGlDtsva+ ++ ++ g ev+av++d+Gq+ ed++ ++++al +Ga++a+v+Dar+ef+++y ++a
  NCBI__GCF_000015305.1:WP_011780511.1   4 RVILAYSGGLDTSVAISWIGKEtGSEVVAVAIDLGQGGEDMEVVRQRALDCGAVEAVVVDARDEFAEQYCLPA 76 
                                           699****************9988************************************************** PP

                             TIGR00032  73 iqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrele 145
                                           i+ na+y ++Y+l++aL+Rpli k lv++a+++g  +vahGctgKGnDqvRFe+ + +l+pdlkv+aPvr+  
  NCBI__GCF_000015305.1:WP_011780511.1  77 IKSNALYMDRYPLVSALSRPLIVKHLVDAAREHGGGVVAHGCTGKGNDQVRFEVGFASLAPDLKVLAPVRDYA 149
                                           ************************************************************************* PP

                             TIGR00032 146 liReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveie 218
                                           ++Re+ i++a+e+ i+++v+k +++siD+n++gr++E+g LE+++ +p++d+y+++ dp+ +   +p++v i+
  NCBI__GCF_000015305.1:WP_011780511.1 150 WTREKAIAFAEENAIPINVTKRSPFSIDQNVWGRAVETGFLEHLWNAPTKDVYDYTEDPTLNW-SSPDEVIIG 221
                                           ************************************************************999.99******* PP

                             TIGR00032 219 FekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltk 291
                                           F+kGvPv+++g+ ++ ++ i+++n  ag++GvGr+D+vEdR++g+KsReiYEap++++Li+Ah +Le+ +l++
  NCBI__GCF_000015305.1:WP_011780511.1 222 FDKGVPVSIDGKPVTVLQAIEQLNARAGAQGVGRLDVVEDRLVGIKSREIYEAPGAMVLITAHTELEHVTLER 294
                                           ************************************************************************* PP

                             TIGR00032 292 dvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsf 364
                                           +  +fk+++++k++el+Y Glwf+pl+ al++++ +tqe+vtG++r+ l+ G+  v gr+s++slYd +l+++
  NCBI__GCF_000015305.1:WP_011780511.1 295 ELGRFKRTTDQKWGELVYDGLWFSPLKTALESFVANTQEHVTGEIRLVLHGGHIAVNGRRSQESLYDFNLATY 367
                                           ************************************************************************* PP

                             TIGR00032 365 ekdkefdqkdaiGfikirglqikvy 389
                                           ++ ++fdq++a+Gf++++gl+ +  
  NCBI__GCF_000015305.1:WP_011780511.1 368 DEGDTFDQSAAKGFVHVHGLSSSLS 392
                                           ********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (400 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 19.67
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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