Alignments for a candidate for argH in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Crocosphaera subtropica ATCC 51142

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_009546728.1 CCE_RS01100 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_000017845.1:WP_009546728.1
          Length = 462

 Score =  730 bits (1884), Expect = 0.0
 Identities = 359/460 (78%), Positives = 410/460 (89%)

Query: 1   MTKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQ 60
           M +++TWS RFE +LHPAI  FNASI FDIELIEYDLTGS AHAKMLA TGIIS  E ++
Sbjct: 1   MRQKKTWSDRFEGSLHPAIVEFNASITFDIELIEYDLTGSIAHAKMLAKTGIISEAEAQK 60

Query: 61  LVAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTR 120
           LV GLEQIRQE+R G F PG+D EDVHFAVE+RLTE+VGDVGKKLHTARSRNDQVGTD R
Sbjct: 61  LVNGLEQIRQEYRDGNFTPGIDQEDVHFAVERRLTELVGDVGKKLHTARSRNDQVGTDIR 120

Query: 121 LYLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQR 180
           LYLRDQIQQI+S+++ FQ VLL  A+++VETLIPGYTHLQRAQP+SLAHHLLAYFQMAQR
Sbjct: 121 LYLRDQIQQIRSQIQAFQQVLLTHAQENVETLIPGYTHLQRAQPISLAHHLLAYFQMAQR 180

Query: 181 DWERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEF 240
           DWERLG++ +R N+SPLGCGALAGTTFPIDRHY+A+LL F+ +Y NSLDGVSDRDFAIEF
Sbjct: 181 DWERLGEIYQRTNVSPLGCGALAGTTFPIDRHYSAELLGFEEVYGNSLDGVSDRDFAIEF 240

Query: 241 LCAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGR 300
           L AASLIMVHLSRL+EE+ILW+S+EF F+ L DSCATGSSIMPQKKNPDVPELVRGK GR
Sbjct: 241 LNAASLIMVHLSRLSEEMILWASQEFGFISLTDSCATGSSIMPQKKNPDVPELVRGKAGR 300

Query: 301 VFGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLA 360
           VFGHLQ MLV+MKGLPLAYNKDLQEDKE +FD V TVK  LEAMT+LL EG+ FR +RL+
Sbjct: 301 VFGHLQGMLVLMKGLPLAYNKDLQEDKEAIFDGVKTVKGCLEAMTVLLGEGITFRKERLS 360

Query: 361 QAVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAF 420
           +AV EDFSNATDVADYLAA+GVPFREAYNLVGKVVKTS+A+GKLLKDL LEEWQ LHP F
Sbjct: 361 EAVAEDFSNATDVADYLAAKGVPFREAYNLVGKVVKTSLASGKLLKDLTLEEWQALHPNF 420

Query: 421 AADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460
            ADIY+AI+P+QVVAARNS+GGTGF Q+ +A+  A+ Q++
Sbjct: 421 EADIYDAIAPKQVVAARNSYGGTGFEQIYQAVERAKQQLE 460


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: 695
Number of extensions: 15
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: 461
Length of database: 462
Length adjustment: 33
Effective length of query: 428
Effective length of database: 429
Effective search space:   183612
Effective search space used:   183612
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_009546728.1 CCE_RS01100 (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.22520.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-212  692.3   0.0     2e-212  692.1   0.0    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009546728.1  CCE_RS01100 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009546728.1  CCE_RS01100 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.1   0.0    2e-212    2e-212       1     454 [.       6     459 ..       6     460 .. 0.99

  Alignments for each domain:
  == domain 1  score: 692.1 bits;  conditional E-value: 2e-212
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               +w++R++++l++a+ efnas++fD el+e+D++gsiah+k+Lak+gi++e ea+kl+++Le++++e+++
  lcl|NCBI__GCF_000017845.1:WP_009546728.1   6 TWSDRFEGSLHPAIVEFNASITFDIELIEYDLTGSIAHAKMLAKTGIISEAEAQKLVNGLEQIRQEYRD 74 
                                               5******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g++++  d+eD+H+avEr+l++ vg dvgkklht+rsRnDqv+td+rlylrd+++++++++++++++l+
  lcl|NCBI__GCF_000017845.1:WP_009546728.1  75 GNFTPGIDQEDVHFAVERRLTELVG-DVGKKLHTARSRNDQVGTDIRLYLRDQIQQIRSQIQAFQQVLL 142
                                               *************************.******************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                                +A+++vetl+pgytHLqrAqPi+laHhllay++m +rD+eRl ++++R+n+sPlG+gAlagt+f+idr
  lcl|NCBI__GCF_000017845.1:WP_009546728.1 143 THAQENVETLIPGYTHLQRAQPISLAHHLLAYFQMAQRDWERLGEIYQRTNVSPLGCGALAGTTFPIDR 211
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               +++aelLgF++v+ nsld+vsdRDf+iE+l+aa+l+mvhlsrl+Ee+il++s+Efgf++l+d++++gss
  lcl|NCBI__GCF_000017845.1:WP_009546728.1 212 HYSAELLGFEEVYGNSLDGVSDRDFAIEFLNAASLIMVHLSRLSEEMILWASQEFGFISLTDSCATGSS 280
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDv El+Rgk+grv+G+l+g+l+++K+lPlaYnkDlqEdkea+fd +ktv+ +le++t+ll 
  lcl|NCBI__GCF_000017845.1:WP_009546728.1 281 IMPQKKNPDVPELVRGKAGRVFGHLQGMLVLMKGLPLAYNKDLQEDKEAIFDGVKTVKGCLEAMTVLLG 349
                                               ********************************************************************8 PP

                                 TIGR00838 346 e.lkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklse 413
                                               e ++++kerl+ea++++f++atd+Adyl++kGvPFRea+++vG+vv++++++Gk l++ltlee+q+l++
  lcl|NCBI__GCF_000017845.1:WP_009546728.1 350 EgITFRKERLSEAVAEDFSNATDVADYLAAKGVPFREAYNLVGKVVKTSLASGKLLKDLTLEEWQALHP 418
                                               88******************************************************************* PP

                                 TIGR00838 414 kleedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               ++e d+++++ ++++v++r+++GGt++e++ +a+e ak++l
  lcl|NCBI__GCF_000017845.1:WP_009546728.1 419 NFEADIYDAIAPKQVVAARNSYGGTGFEQIYQAVERAKQQL 459
                                               **************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (462 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: 00:00:00.02
# Mc/sec: 9.46
//
[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