Alignments for a candidate for argH in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Azospirillum brasilense Sp245

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate AZOBR_RS16935 AZOBR_RS16935 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__azobra:AZOBR_RS16935
          Length = 480

 Score =  427 bits (1098), Expect = e-124
 Identities = 221/453 (48%), Positives = 298/453 (65%), Gaps = 1/453 (0%)

Query: 7   KLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAG 66
           ++WGGRF  G A  +E   ASI FD++LA+ D+ GS AH  ML  +GII+Q DA  I+ G
Sbjct: 25  QMWGGRFARGPAAIMERINASIGFDKRLADQDIAGSKAHAAMLARQGIITQADADAIREG 84

Query: 67  LEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLK 126
           L+ + EE  +G   F V  EDIHMN+E+ L   IG  A +LHT RSRNDQVATD  L+++
Sbjct: 85  LDRVKEEIDSGAFTFKVELEDIHMNVEARLAELIGEPAKRLHTGRSRNDQVATDFKLWVR 144

Query: 127 AKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSER 186
             LD   + L  L+  L+DLA+KH  T+MPG+THLQ AQP+SFGHHL+AY  MF RD  R
Sbjct: 145 DALDRADQGLKALQAALIDLAEKHTDTVMPGFTHLQAAQPVSFGHHLLAYVEMFGRDRGR 204

Query: 187 FIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNA 246
                   +  PLG+AALAGT +PIDR MTA+ +GF  P +NSLDAVSDRDF LE+L+ A
Sbjct: 205 LRDARARLNECPLGSAALAGTPYPIDRFMTAEALGFDRPTANSLDAVSDRDFALEYLAAA 264

Query: 247 SILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYAN 306
           SI  MH+SR  EE++ WCS +++F+ L+D F+TGSSIMPQKKNPD AEL+R K+GRV  +
Sbjct: 265 SICGMHLSRFAEEIVLWCSAQFRFIKLTDAFTTGSSIMPQKKNPDAAELVRAKAGRVIGS 324

Query: 307 LFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQK 366
           L  LL  MK LPLAY+KD+QEDKE +F+  +T+ + +  + GM+  M  N   + E+T +
Sbjct: 325 LNSLLVAMKGLPLAYSKDMQEDKEPVFEADDTLALCIAAMEGMVRDMQPNVPALREATDR 384

Query: 367 DFSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDV 425
            F NAT+LAD+L  +  +PFR+AH I G+ +         L  + LE  Q I   I E V
Sbjct: 385 GFLNATDLADWLVRELNIPFREAHHITGRAVKAAEDKRVGLTALTLEELQAIEPRITESV 444

Query: 426 YETLKSHTAVERRHSLGGTGFEQVKWQIAEAKK 458
           +  L    +++ R S GG    +V+  +A A++
Sbjct: 445 FPALSIEASLDSRRSFGGASPVRVREAVAAARE 477


Lambda     K      H
   0.318    0.132    0.378 

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: 17
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: 460
Length of database: 480
Length adjustment: 33
Effective length of query: 427
Effective length of database: 447
Effective search space:   190869
Effective search space used:   190869
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS16935 AZOBR_RS16935 (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.7158.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-187  608.6   0.0   4.8e-187  608.4   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS16935  AZOBR_RS16935 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS16935  AZOBR_RS16935 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  608.4   0.0  4.8e-187  4.8e-187       1     453 [.      26     478 ..      26     480 .] 0.99

  Alignments for each domain:
  == domain 1  score: 608.4 bits;  conditional E-value: 4.8e-187
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               +wggR+++++   +++ nas+ fDk+la +Di gs+ah+++La++gi+t+ +a+ ++e+L+++kee+++
  lcl|FitnessBrowser__azobra:AZOBR_RS16935  26 MWGGRFARGPAAIMERINASIGFDKRLADQDIAGSKAHAAMLARQGIITQADADAIREGLDRVKEEIDS 94 
                                               6******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g+++++v+ eDiH++vE++l + +g + +k+lhtgrsRnDqvatd++l++rd++++  + lk+l++al+
  lcl|FitnessBrowser__azobra:AZOBR_RS16935  95 GAFTFKVELEDIHMNVEARLAELIG-EPAKRLHTGRSRNDQVATDFKLWVRDALDRADQGLKALQAALI 162
                                               *************************.6666*************************************** PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               ++Aek+++t+mpg+tHLq AqP++++Hhllay+em+ rD  Rl da  R+n++PlGs+Alagt ++idr
  lcl|FitnessBrowser__azobra:AZOBR_RS16935 163 DLAEKHTDTVMPGFTHLQAAQPVSFGHHLLAYVEMFGRDRGRLRDARARLNECPLGSAALAGTPYPIDR 231
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                                ++ae LgFd+ ++nsldavsdRDf++E l+aa+++ +hlsr+aEe++l++s+ f f++l+d++++gss
  lcl|FitnessBrowser__azobra:AZOBR_RS16935 232 FMTAEALGFDRPTANSLDAVSDRDFALEYLAAASICGMHLSRFAEEIVLWCSAQFRFIKLTDAFTTGSS 300
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpD+aEl+R+k+grviG+l +ll+ +K+lPlaY kD+qEdke++f+a +t+  ++ +++g+++
  lcl|FitnessBrowser__azobra:AZOBR_RS16935 301 IMPQKKNPDAAELVRAKAGRVIGSLNSLLVAMKGLPLAYSKDMQEDKEPVFEADDTLALCIAAMEGMVR 369
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklse 413
                                               +++ n   l+ea+ ++f +atdlAd+lvr+  +PFReah+i+G++v++a++k ++l+ ltleelq++++
  lcl|FitnessBrowser__azobra:AZOBR_RS16935 370 DMQPNVPALREATDRGFLNATDLADWLVRElNIPFREAHHITGRAVKAAEDKRVGLTALTLEELQAIEP 438
                                               ********************************************************************* PP

                                 TIGR00838 414 kleedvlevldleeavekrdakGGtakeevekaieeakae 453
                                               +++e v+ +l++e +++ r++ GG+++ +v++a+++a+++
  lcl|FitnessBrowser__azobra:AZOBR_RS16935 439 RITESVFPALSIEASLDSRRSFGGASPVRVREAVAAARER 478
                                               ************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (480 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: 9.69
//
[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