Alignments for a candidate for argH in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Synechococcus elongatus PCC 7942

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate Synpcc7942_2475 Synpcc7942_2475 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__SynE:Synpcc7942_2475
          Length = 474

 Score =  702 bits (1812), Expect = 0.0
 Identities = 351/456 (76%), Positives = 394/456 (86%)

Query: 5   QTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAG 64
           Q WS RFE+ALHPAI  FNASIGFD+ LIEYDLTGSQAHA+MLA   IIS EEGE +VAG
Sbjct: 16  QPWSDRFETALHPAIVVFNASIGFDLALIEYDLTGSQAHAQMLAEQDIISREEGEAIVAG 75

Query: 65  LEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLR 124
           LEQIR E+R G+F PG+DAEDVHFAVE+RLTE++GDVGKKLHTARSRNDQVGTDTRLYLR
Sbjct: 76  LEQIRSEYRTGQFQPGLDAEDVHFAVERRLTELLGDVGKKLHTARSRNDQVGTDTRLYLR 135

Query: 125 DQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWER 184
           D++  I+ +LR++Q VLL  AE+H+ETLIPGYTHLQRAQP+SLAHHL AY +MA+RDWER
Sbjct: 136 DRVDHIRQQLRDYQRVLLSQAEQHLETLIPGYTHLQRAQPLSLAHHLHAYLEMAERDWER 195

Query: 185 LGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAA 244
           LGD+ +R+N SPLG GALAGTTFPIDR  TA LL F+ IYANSLD VSDRD  +EFL AA
Sbjct: 196 LGDLRKRLNTSPLGAGALAGTTFPIDRQRTAALLGFERIYANSLDAVSDRDSLVEFLAAA 255

Query: 245 SLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGH 304
           SLIMVHLSRLAEEVILW+SEEFRFV L D CATGSSIMPQKKNPDVPELVRGKTGRVFGH
Sbjct: 256 SLIMVHLSRLAEEVILWASEEFRFVRLSDRCATGSSIMPQKKNPDVPELVRGKTGRVFGH 315

Query: 305 LQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVT 364
           LQA+LV++KGLPLAYNKDLQEDKEGLFD+V TV++ LEAMTIL  EGL F+  RLA AV 
Sbjct: 316 LQALLVVLKGLPLAYNKDLQEDKEGLFDAVQTVESCLEAMTILFAEGLSFQPDRLAAAVE 375

Query: 365 EDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADI 424
            DFSNATDVADYLAARGVPFREAYNLVG+VV+T +  GKLLKDL L EWQ LHP F ADI
Sbjct: 376 ADFSNATDVADYLAARGVPFREAYNLVGRVVRTCLEQGKLLKDLSLAEWQALHPQFEADI 435

Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460
           Y AI+P+QVVAARNS GGTGF QV  AL + R +++
Sbjct: 436 YTAIAPQQVVAARNSLGGTGFEQVRSALASVRQRLE 471


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: 691
Number of extensions: 22
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: 474
Length adjustment: 33
Effective length of query: 428
Effective length of database: 441
Effective search space:   188748
Effective search space used:   188748
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 Synpcc7942_2475 Synpcc7942_2475 (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.21932.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-199  649.5   0.0   1.8e-199  649.3   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2475  Synpcc7942_2475 argininosuccinat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2475  Synpcc7942_2475 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  649.3   0.0  1.8e-199  1.8e-199       2     454 ..      18     470 ..      17     471 .. 0.99

  Alignments for each domain:
  == domain 1  score: 649.3 bits;  conditional E-value: 1.8e-199
                                 TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg 70 
                                               w++R++ +l++a+  fnas+ fD  l+e+D++gs ah+++La++ i+++ee + ++++Le++++e++ g
  lcl|FitnessBrowser__SynE:Synpcc7942_2475  18 WSDRFETALHPAIVVFNASIGFDLALIEYDLTGSQAHAQMLAEQDIISREEGEAIVAGLEQIRSEYRTG 86 
                                               9******************************************************************** PP

                                 TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalve 139
                                               ++++  daeD+H+avEr+l++ +g dvgkklht+rsRnDqv+td rlylrd+v++++++l+d +++l+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_2475  87 QFQPGLDAEDVHFAVERRLTELLG-DVGKKLHTARSRNDQVGTDTRLYLRDRVDHIRQQLRDYQRVLLS 154
                                               ************************.******************************************** PP

                                 TIGR00838 140 kAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidre 208
                                               +Ae++ etl+pgytHLqrAqP++laHhl ay em erD+eRl d  kR+n+sPlG+gAlagt+f+idr+
  lcl|FitnessBrowser__SynE:Synpcc7942_2475 155 QAEQHLETLIPGYTHLQRAQPLSLAHHLHAYLEMAERDWERLGDLRKRLNTSPLGAGALAGTTFPIDRQ 223
                                               ********************************************************************* PP

                                 TIGR00838 209 llaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssi 277
                                               ++a+lLgF+++++nsldavsdRD ++E+l+aa+l+mvhlsrlaEe+il++seEf fv lsd++++gssi
  lcl|FitnessBrowser__SynE:Synpcc7942_2475 224 RTAALLGFERIYANSLDAVSDRDSLVEFLAAASLIMVHLSRLAEEVILWASEEFRFVRLSDRCATGSSI 292
                                               ********************************************************************* PP

                                 TIGR00838 278 mPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllke 346
                                               mPqKKnpDv El+Rgktgrv+G+l++ll++lK+lPlaYnkDlqEdke+lfda++tve++le++t+l++e
  lcl|FitnessBrowser__SynE:Synpcc7942_2475 293 MPQKKNPDVPELVRGKTGRVFGHLQALLVVLKGLPLAYNKDLQEDKEGLFDAVQTVESCLEAMTILFAE 361
                                               ******************************************************************988 PP

                                 TIGR00838 347 .lkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                                l ++ +rl+ a++++f++atd+Adyl+++GvPFRea+++vG+vv++++e+Gk l++l+l+e+q+l+++
  lcl|FitnessBrowser__SynE:Synpcc7942_2475 362 gLSFQPDRLAAAVEADFSNATDVADYLAARGVPFREAYNLVGRVVRTCLEQGKLLKDLSLAEWQALHPQ 430
                                               8******************************************************************** PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               +e d+++++ ++++v++r++ GGt++e+v++a+++++++l
  lcl|FitnessBrowser__SynE:Synpcc7942_2475 431 FEADIYTAIAPQQVVAARNSLGGTGFEQVRSALASVRQRL 470
                                               ***********************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (474 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.51
//
[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