Alignments for a candidate for argG in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Methanobacterium lacus AL-21

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_013643859.1 METBO_RS01305 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000191585.1:WP_013643859.1
          Length = 393

 Score =  318 bits (815), Expect = 2e-91
 Identities = 175/386 (45%), Positives = 245/386 (63%), Gaps = 7/386 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGE-EVEEAREKALRTGASKAIALD 60
           K+VLA+SGGLDTS+ +K L+E Y  EV+    D+GQ E E+E   + A   G  K   +D
Sbjct: 3   KVVLAFSGGLDTSVCVKLLQEKYNMEVVTACVDVGQPEDEIERPAQVANNIGVKKHYTID 62

Query: 61  LKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGN 120
            K EF  +F+F  ++A A+YEGY L  TS+ARPLIA  +V +A++E A+AIAHG TGKGN
Sbjct: 63  AKHEFAEEFIFRAIKANAMYEGYPL-STSLARPLIAMKIVELAKKEQADAIAHGCTGKGN 121

Query: 121 DQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLH 180
           DQ RFE T  +      +IAP R+ +    +EM  YA  + IPVP   +K YS+D NL  
Sbjct: 122 DQFRFETTIRSSSV-CDIIAPVRDLNLTRTEEM-DYAVKNDIPVP--SDKLYSIDENLWG 177

Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240
            S EG +LEDP  E P+  F  TQ  E APD P+ + V F EG PVA++GE ++   ++Q
Sbjct: 178 RSIEGDILEDPMVETPEEAFEWTQSTENAPDEPQKLTVTFEEGVPVAIDGEMMNALEIIQ 237

Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300
             N I G HG+GRVDI+E+R +G+KSR  YETPG  +L  A +A+E LTL RE L   + 
Sbjct: 238 EANRIAGLHGIGRVDIIEDRIIGLKSRENYETPGAELLITAHKALEQLTLTREELKFGET 297

Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360
           ++  Y+ELVY G W+ P RE L    D++   V+G   LKL+KG++ ++ R++P SLY +
Sbjct: 298 VTQAYSELVYNGLWHEPLREDLDCIIDNMQLRVSGDVILKLHKGSIRILARESPYSLYSE 357

Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALR 386
           + VSF++    DQ++  G +K   L+
Sbjct: 358 EAVSFEDK-EMDQREIAGMVKNYGLQ 382


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: 375
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: 400
Length of database: 393
Length adjustment: 31
Effective length of query: 369
Effective length of database: 362
Effective search space:   133578
Effective search space used:   133578
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 WP_013643859.1 METBO_RS01305 (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.6878.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.3e-171  554.5   0.2   9.3e-171  554.3   0.2    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013643859.1  METBO_RS01305 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013643859.1  METBO_RS01305 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.3   0.2  9.3e-171  9.3e-171       1     394 []       3     391 ..       3     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 554.3 bits;  conditional E-value: 9.3e-171
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               kvvla+sGGlDtsv++kll+ek ++ev++++vdvGqpe+++++ ++ a ++G++k+y+iDa++ef++++
  lcl|NCBI__GCF_000191585.1:WP_013643859.1   3 KVVLAFSGGLDTSVCVKLLQEKyNMEVVTACVDVGQPEDEIERPAQVANNIGVKKHYTIDAKHEFAEEF 71 
                                               8******************************************************************** PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                               +f+ai+ana+yeg Y+lst+LaRplia k+ve akke a+a+ahGctgKGnDq+RFe++i+ + +  ++
  lcl|NCBI__GCF_000191585.1:WP_013643859.1  72 IFRAIKANAMYEG-YPLSTSLARPLIAMKIVELAKKEQADAIAHGCTGKGNDQFRFETTIR-SSSVCDI 138
                                               *************.***********************************************.77889** PP

                                 TIGR00032 138 iaPvreleliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpie 206
                                               iaPvr+l+l+R+ee++ya ++ i+vp++  k ysiDenl+grsiE+++LEdp++e pe+++e+++  +e
  lcl|NCBI__GCF_000191585.1:WP_013643859.1 139 IAPVRDLNLTRTEEMDYAVKNDIPVPSD--KLYSIDENLWGRSIEGDILEDPMVETPEEAFEWTQ-STE 204
                                               *************************998..8**********************************.566 PP

                                 TIGR00032 207 ktedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapall 275
                                               + +dep++++++Fe+GvPva++ge+++++e+i++an+iag hG+Gr+Di+EdRiiglKsRe+YE+p++ 
  lcl|NCBI__GCF_000191585.1:WP_013643859.1 205 NAPDEPQKLTVTFEEGVPVAIDGEMMNALEIIQEANRIAGLHGIGRVDIIEDRIIGLKSRENYETPGAE 273
                                               666****************************************************************** PP

                                 TIGR00032 276 lLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGn 344
                                               lLi+Ahk+Le+l+lt+++l+f e+v++ ysel+Y+Glw++pl+e+ld +i+++q rv+G v +kl+kG+
  lcl|NCBI__GCF_000191585.1:WP_013643859.1 274 LLITAHKALEQLTLTREELKFGETVTQAYSELVYNGLWHEPLREDLDCIIDNMQLRVSGDVILKLHKGS 342
                                               ********************************************************************* PP

                                 TIGR00032 345 aivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvyreklk 394
                                                ++++r+s+yslY+ee vsfe dke+dq++ +G++k++glq++ y++++k
  lcl|NCBI__GCF_000191585.1:WP_013643859.1 343 IRILARESPYSLYSEEAVSFE-DKEMDQREIAGMVKNYGLQAACYQKVCK 391
                                               *********************.***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (393 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.95
//
[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