Alignments for a candidate for argH in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Herbaspirillum autotrophicum IAM 14942

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_050465259.1 AKL27_RS23255 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_001189915.1:WP_050465259.1
          Length = 464

 Score =  449 bits (1156), Expect = e-131
 Identities = 228/457 (49%), Positives = 308/457 (67%), Gaps = 1/457 (0%)

Query: 3   KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62
           K + WS RF   +   + R+ AS+ FD  L  +D+ GS AHA+MLAH  II++++   + 
Sbjct: 8   KGEAWSARFSEPVSDLVKRYTASVFFDKRLARFDIEGSLAHAEMLAHQNIINAQDLADIR 67

Query: 63  AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122
            G+EQI  E   G F   +D EDVH  +EKRLTE+VGD GK+LHT RSRNDQV TD RLY
Sbjct: 68  RGMEQISAEIDAGSFEWLLDLEDVHLNIEKRLTELVGDAGKRLHTGRSRNDQVATDIRLY 127

Query: 123 LRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDW 182
           +R  I  I   LR+ +  LLD+AE+H +T++PG+TH+Q AQP++  HH+LAY +M  RD 
Sbjct: 128 IRAAIDDINGLLRDLRSALLDLAEQHADTILPGFTHMQVAQPITFGHHILAYVEMFGRDA 187

Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242
           ER+ D  +RVN  PLG  ALAGTTFPIDR   A+ L FD++  NSLD VSDRDFAIEF  
Sbjct: 188 ERMTDARKRVNRLPLGAAALAGTTFPIDRLRVAQTLGFDDVCRNSLDAVSDRDFAIEFCA 247

Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302
           AA+L+M H+SR++EE+++W S    F+ + D   TGSSIMPQKKNPDVPEL RGKTGRV 
Sbjct: 248 AAALVMTHISRMSEELVIWMSPRIGFIDIADRFCTGSSIMPQKKNPDVPELARGKTGRVN 307

Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362
           GHL A+L +MKG PLAYNKD QEDKE LFD+V+T+  +L     + R G+  + + +  A
Sbjct: 308 GHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLTDTLRIFADMAR-GITVKPEAMRAA 366

Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAA 422
             + ++ ATD+ADYL  +G+PFR+A+  V + V++ +     L DL LE+ +   P   A
Sbjct: 367 ALQGYATATDLADYLVKKGLPFRDAHEAVARAVRSCVDLNCDLSDLTLEQLKVFSPLIEA 426

Query: 423 DIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
           DI+  ++    VAAR+  GGT   QV +A+ A R ++
Sbjct: 427 DIFAVLTLEGSVAARDHIGGTAPNQVRQAIAAIRKEL 463


Lambda     K      H
   0.320    0.135    0.384 

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: 502
Number of extensions: 17
Number of successful extensions: 2
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: 461
Length of database: 464
Length adjustment: 33
Effective length of query: 428
Effective length of database: 431
Effective search space:   184468
Effective search space used:   184468
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_050465259.1 AKL27_RS23255 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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/TIGR00838.hmm
# target sequence database:        /tmp/gapView.1577502.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-189  615.7   0.1   3.3e-189  615.5   0.1    1.0  1  NCBI__GCF_001189915.1:WP_050465259.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050465259.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  615.5   0.1  3.3e-189  3.3e-189       2     454 ..      12     463 ..      11     464 .] 1.00

  Alignments for each domain:
  == domain 1  score: 615.5 bits;  conditional E-value: 3.3e-189
                             TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklel 74 
                                           w+ R+++ +++ v++++as+ fDk+la+ Diegs+ah+++La+++i+++++ +++++++e++  e+++g++e+
  NCBI__GCF_001189915.1:WP_050465259.1  12 WSARFSEPVSDLVKRYTASVFFDKRLARFDIEGSLAHAEMLAHQNIINAQDLADIRRGMEQISAEIDAGSFEW 84 
                                           9************************************************************************ PP

                             TIGR00838  75 evdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevet 147
                                             d eD+Hl++E++l++ vg d+gk+lhtgrsRnDqvatd+rly+r++++++   l+dl++al+++Ae++ +t
  NCBI__GCF_001189915.1:WP_050465259.1  85 LLDLEDVHLNIEKRLTELVG-DAGKRLHTGRSRNDQVATDIRLYIRAAIDDINGLLRDLRSALLDLAEQHADT 156
                                           ********************.**************************************************** PP

                             TIGR00838 148 lmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavv 220
                                           ++pg+tH+q AqPit++Hh+lay+em+ rD eR++da kRvn+ PlG++Alagt+f+idr ++a++LgFd+v+
  NCBI__GCF_001189915.1:WP_050465259.1 157 ILPGFTHMQVAQPITFGHHILAYVEMFGRDAERMTDARKRVNRLPLGAAALAGTTFPIDRLRVAQTLGFDDVC 229
                                           ************************************************************************* PP

                             TIGR00838 221 ensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgk 293
                                           +nsldavsdRDf+iE+ +aaal+m+h+sr++Eel+++ s  +gf++++d++++gssimPqKKnpDv El+Rgk
  NCBI__GCF_001189915.1:WP_050465259.1 230 RNSLDAVSDRDFAIEFCAAAALVMTHISRMSEELVIWMSPRIGFIDIADRFCTGSSIMPQKKNPDVPELARGK 302
                                           ************************************************************************* PP

                             TIGR00838 294 tgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalat 366
                                           tgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++t++++l++++ + + ++v+ e ++ aa +++a+at
  NCBI__GCF_001189915.1:WP_050465259.1 303 TGRVNGHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLTDTLRIFADMARGITVKPEAMRAAALQGYATAT 375
                                           ************************************************************************* PP

                             TIGR00838 367 dlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGta 439
                                           dlAdylv+kG+PFR+ahe v ++v+++++   +l++ltle+l+ +s+ +e d++ vl+le +v++rd +GGta
  NCBI__GCF_001189915.1:WP_050465259.1 376 DLADYLVKKGLPFRDAHEAVARAVRSCVDLNCDLSDLTLEQLKVFSPLIEADIFAVLTLEGSVAARDHIGGTA 448
                                           ************************************************************************* PP

                             TIGR00838 440 keevekaieeakael 454
                                           +++v++ai+++++el
  NCBI__GCF_001189915.1:WP_050465259.1 449 PNQVRQAIAAIRKEL 463
                                           *********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (464 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: 00:00:00.01
# Mc/sec: 16.34
//
[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