Alignments for a candidate for argH in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Cupriavidus basilensis 4G11

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate RR42_RS15925 RR42_RS15925 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__Cup4G11:RR42_RS15925
          Length = 469

 Score =  426 bits (1094), Expect = e-123
 Identities = 226/463 (48%), Positives = 296/463 (63%), Gaps = 7/463 (1%)

Query: 3   KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62
           K + WS RF   +   + R+ AS+ FD  L  +D+ GS AHA MLA  GII+  +  ++ 
Sbjct: 8   KGEAWSARFSEPMSDLVKRYTASVFFDKRLALFDIQGSLAHAAMLAKQGIIAEADRAEIE 67

Query: 63  AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122
            G+ QIR E   G F   +D EDVH  +E RLT +VGD GK+LHT RSRNDQV TD RL+
Sbjct: 68  RGMTQIRGEIEAGGFEWKLDLEDVHLNIEARLTALVGDAGKRLHTGRSRNDQVATDIRLW 127

Query: 123 LRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDW 182
           LR +I  I   L   +G LLD+AEK+ +T++PG+THLQ AQPV+  HHLLAY +M  RD 
Sbjct: 128 LRSEIDTIIGLLGALRGALLDLAEKNADTILPGFTHLQVAQPVTFGHHLLAYVEMFTRDA 187

Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242
           ER+ D  RRVN  PLG  ALAGT++PIDR + A+ L FD +  NSLD VSDRDFAIEF  
Sbjct: 188 ERMADCRRRVNRLPLGAAALAGTSYPIDREFVAQQLGFDGVCRNSLDAVSDRDFAIEFCA 247

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

Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362
           GHL  +L +MKG PLAYNKD QEDKE LFD+V+TV  +L     ++  G+  +   +  A
Sbjct: 308 GHLIGLLTLMKGQPLAYNKDNQEDKEPLFDTVDTVADTLRIFADMV-PGISVKPDAMRAA 366

Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQL------ 416
             + ++ ATD+ADYL   G+PFR+A+  V   V+        L DL + E +++      
Sbjct: 367 ALQGYATATDLADYLVKHGLPFRDAHEAVAHAVRACDDRRCDLADLTVAELREVTGLGDK 426

Query: 417 HPAFAADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
                 D++  ++    VAARN  GGT   QV  A+ AARA +
Sbjct: 427 AALIGDDVHAVLTLEGSVAARNHIGGTAPAQVRAAIAAARATL 469


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: 521
Number of extensions: 21
Number of successful extensions: 3
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: 469
Length adjustment: 33
Effective length of query: 428
Effective length of database: 436
Effective search space:   186608
Effective search space used:   186608
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 RR42_RS15925 RR42_RS15925 (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.24012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-186  606.1   0.0   2.7e-186  605.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS15925  RR42_RS15925 argininosuccinate l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS15925  RR42_RS15925 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.9   0.0  2.7e-186  2.7e-186       2     453 ..      12     468 ..      11     469 .] 0.98

  Alignments for each domain:
  == domain 1  score: 605.9 bits;  conditional E-value: 2.7e-186
                                 TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg 70 
                                               w+ R+++ +++ v++++as+ fDk+la  Di+gs+ah+++Lak+gi+ e +++++++++++++ e+++g
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925  12 WSARFSEPMSDLVKRYTASVFFDKRLALFDIQGSLAHAAMLAKQGIIAEADRAEIERGMTQIRGEIEAG 80 
                                               9******************************************************************** PP

                                 TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalve 139
                                                +e++ d eD+Hl++E++l++ vg d+gk+lhtgrsRnDqvatd+rl+lr ++++++  l +l+ al++
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925  81 GFEWKLDLEDVHLNIEARLTALVG-DAGKRLHTGRSRNDQVATDIRLWLRSEIDTIIGLLGALRGALLD 148
                                               ************************.******************************************** PP

                                 TIGR00838 140 kAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidre 208
                                               +Aek+ +t++pg+tHLq AqP+t++Hhllay+em++rD eR+ d  +Rvn+ PlG++Alagts++idre
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925 149 LAEKNADTILPGFTHLQVAQPVTFGHHLLAYVEMFTRDAERMADCRRRVNRLPLGAAALAGTSYPIDRE 217
                                               ********************************************************************* PP

                                 TIGR00838 209 llaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssi 277
                                               ++a++LgFd v++nsldavsdRDf+iE+ +aaal+m+h+sr++Eel+++ s  +gf++++d++++gssi
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925 218 FVAQQLGFDGVCRNSLDAVSDRDFAIEFCAAAALVMTHISRFSEELVIWMSPRVGFIDIADRFCTGSSI 286
                                               ********************************************************************* PP

                                 TIGR00838 278 mPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllke 346
                                               mPqKKnpDv El+Rgktgrv+G+l+gllt++K++PlaYnkD qEdke+lfd+++tv ++l++++ ++  
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925 287 MPQKKNPDVPELARGKTGRVNGHLIGLLTLMKGQPLAYNKDNQEDKEPLFDTVDTVADTLRIFADMVPG 355
                                               ********************************************************************* PP

                                 TIGR00838 347 lkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqkls... 412
                                               + v+ + ++ aa +++a+atdlAdylv++G+PFR+ahe v ++v+++ ++  +l +lt++el+++    
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925 356 ISVKPDAMRAAALQGYATATDLADYLVKHGLPFRDAHEAVAHAVRACDDRRCDLADLTVAELREVTglg 424
                                               **************************************************99*********99874222 PP

                                 TIGR00838 413 ...ekleedvlevldleeavekrdakGGtakeevekaieeakae 453
                                                    + +dv+ vl+le +v++r+ +GGta+++v+ ai++a+a+
  lcl|FitnessBrowser__Cup4G11:RR42_RS15925 425 dkaALIGDDVHAVLTLEGSVAARNHIGGTAPAQVRAAIAAARAT 468
                                               222568999*******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (469 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: 00:00:00.01
# Mc/sec: 12.38
//
[ok]

This GapMind analysis is from Apr 09 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