Alignments for a candidate for argH in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Marinobacter adhaerens HP15

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate GFF244 HP15_243 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__Marino:GFF244
          Length = 469

 Score =  465 bits (1197), Expect = e-135
 Identities = 238/458 (51%), Positives = 311/458 (67%), Gaps = 1/458 (0%)

Query: 2   TKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQL 61
           + E+ W  RF       + +F AS+GFD  L  +D+TGS AHA MLA  G+++++E +Q+
Sbjct: 12  SSEKPWGGRFSEPTDAFVEKFTASVGFDQRLYHHDITGSIAHATMLAEVGVLTTDERDQI 71

Query: 62  VAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRL 121
           + GL+ ++ +   G F   V  EDVH  +E RLT+ +G  GKKLHT RSRNDQV TD RL
Sbjct: 72  IEGLKGVKADIEAGNFQWSVSLEDVHMNIEARLTDRIGITGKKLHTGRSRNDQVATDIRL 131

Query: 122 YLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRD 181
           YLRD+I  I  EL+  Q  LLD+AE+  +T++PG+THLQ AQPV+  HHLLA+++M  RD
Sbjct: 132 YLRDEIDVIAEELKRLQTGLLDLAEREADTIMPGFTHLQTAQPVTFGHHLLAWYEMLVRD 191

Query: 182 WERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFL 241
            ERL D  +RVN+ PLG  ALAGTT+PIDR  TA+LL FD    NSLD VSDRDFAIEF 
Sbjct: 192 AERLQDCRKRVNVMPLGAAALAGTTYPIDRAMTARLLGFDRPTENSLDSVSDRDFAIEFC 251

Query: 242 CAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRV 301
             A+L+M HLSR +EE++LW+S +F F+ L D   TGSSIMPQKKNPDVPELVRGKTGRV
Sbjct: 252 SFAALLMTHLSRFSEELVLWTSAQFDFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRV 311

Query: 302 FGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQ 361
            GHL ++L +MK  PLAYNKD QEDKE LFD+V+T+K  L+A   ++   +  +   +  
Sbjct: 312 NGHLISLLTLMKSQPLAYNKDNQEDKEPLFDTVDTIKGCLKAYADMI-PAIRSKADNMRV 370

Query: 362 AVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFA 421
           A    FS ATD+ADYL  +GVPFR+A+ +VGK V   +A G+ L D+ LEE QQ      
Sbjct: 371 AAKRGFSTATDLADYLVKKGVPFRDAHEIVGKSVAFGVAEGRDLSDMTLEELQQFSDHIG 430

Query: 422 ADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
           AD++  ++    V AR+  GGT   QV  A+  AR Q+
Sbjct: 431 ADVFHVLTLEGSVQARDHLGGTAPDQVRAAVGRARNQL 468


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: 529
Number of extensions: 21
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: 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 GFF244 HP15_243 (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.10973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.4e-200  651.4   0.0     5e-200  651.2   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF244  HP15_243 argininosuccinate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF244  HP15_243 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.2   0.0    5e-200    5e-200       2     454 ..      17     468 ..      16     469 .] 0.99

  Alignments for each domain:
  == domain 1  score: 651.2 bits;  conditional E-value: 5e-200
                          TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevd 77 
                                        wggR+++ +d  v++f+as+ fD++l+++Di+gsiah+++La++g+lt++e++++ie+L+ +k ++++g+++++v+
  lcl|FitnessBrowser__Marino:GFF244  17 WGGRFSEPTDAFVEKFTASVGFDQRLYHHDITGSIAHATMLAEVGVLTTDERDQIIEGLKGVKADIEAGNFQWSVS 92 
                                        9*************************************************************************** PP

                          TIGR00838  78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgyt 153
                                         eD+H+++E++l+d++g   gkklhtgrsRnDqvatd+rlylrd+++ +ae+lk l++ l+++Ae+e +t+mpg+t
  lcl|FitnessBrowser__Marino:GFF244  93 LEDVHMNIEARLTDRIG-ITGKKLHTGRSRNDQVATDIRLYLRDEIDVIAEELKRLQTGLLDLAEREADTIMPGFT 167
                                        *****************.999******************************************************* PP

                          TIGR00838 154 HLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsd 229
                                        HLq AqP+t++Hhlla+ eml rD eRl+d  kRvn+ PlG++Alagt+++idr ++a+lLgFd+ +ensld+vsd
  lcl|FitnessBrowser__Marino:GFF244 168 HLQTAQPVTFGHHLLAWYEMLVRDAERLQDCRKRVNVMPLGAAALAGTTYPIDRAMTARLLGFDRPTENSLDSVSD 243
                                        **************************************************************************** PP

                          TIGR00838 230 RDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltgll 305
                                        RDf+iE+ s aallm+hlsr++Eel+l++s+ f+f++l+d++++gssimPqKKnpDv El+Rgktgrv+G+l++ll
  lcl|FitnessBrowser__Marino:GFF244 244 RDFAIEFCSFAALLMTHLSRFSEELVLWTSAQFDFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRVNGHLISLL 319
                                        **************************************************************************** PP

                          TIGR00838 306 tilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFRe 381
                                        t++K++PlaYnkD qEdke+lfd+++t++ +l++ + ++  ++ + ++++ aak++f++atdlAdylv+kGvPFR+
  lcl|FitnessBrowser__Marino:GFF244 320 TLMKSQPLAYNKDNQEDKEPLFDTVDTIKGCLKAYADMIPAIRSKADNMRVAAKRGFSTATDLADYLVKKGVPFRD 395
                                        **************************************************************************** PP

                          TIGR00838 382 aheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeakael 454
                                        aheivG+ va  +++G +l+++tleelq++s ++  dv++vl+le +v++rd  GGta+++v+ a+  a+++l
  lcl|FitnessBrowser__Marino:GFF244 396 AHEIVGKSVAFGVAEGRDLSDMTLEELQQFSDHIGADVFHVLTLEGSVQARDHLGGTAPDQVRAAVGRARNQL 468
                                        *******************************************************************999886 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.73
//
[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