Alignments for a candidate for argH in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Burkholderia phytofirmans PsJN

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate BPHYT_RS05210 BPHYT_RS05210 argininosuccinate lyase

Query= BRENDA::Q9LAE5
         (461 letters)



>FitnessBrowser__BFirm:BPHYT_RS05210
          Length = 468

 Score =  437 bits (1123), Expect = e-127
 Identities = 235/461 (50%), Positives = 304/461 (65%), Gaps = 5/461 (1%)

Query: 3   KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62
           K + WS RF   +   + R+ +S+ FD  L   D+ GS AHA MLA   II++++   + 
Sbjct: 8   KGEAWSARFSEPMSELVKRYTSSVFFDKRLALVDIEGSLAHASMLAAQKIIAADDLAAIQ 67

Query: 63  AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122
            G+ QI+ E  +G+F   +D EDVH  +E RLT ++GD GK+LHT RSRNDQV TD RL+
Sbjct: 68  RGMAQIKGEIERGEFEWQLDLEDVHLNIEARLTALIGDAGKRLHTGRSRNDQVATDIRLW 127

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

Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242
           ER+ D  +RVN  PLG  ALAGT++PIDRH  AK L FD I ANSLD VSDRDFAIEF  
Sbjct: 188 ERMIDCRKRVNRLPLGAAALAGTSYPIDRHAVAKTLGFDGICANSLDAVSDRDFAIEFTA 247

Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302
           A++L+M H+SR +EE++LW S    F+ L D   TGSSIMPQKKNPDVPEL RGKTGRV 
Sbjct: 248 ASALVMTHVSRFSEELVLWMSPRVGFIDLADRFCTGSSIMPQKKNPDVPELARGKTGRVN 307

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

Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFA- 421
             + FS ATD+ADYL  RG+PFR+A+  V   V+     G  L DL LEE ++  P  A 
Sbjct: 367 ALQGFSTATDLADYLVKRGLPFRDAHEAVALAVRVCADRGCDLADLTLEEMRKELPNVAH 426

Query: 422 ---ADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
               D++  ++    VA+RN  GGT   QV  A+ AARA +
Sbjct: 427 LIGEDVFSYLTLEGSVASRNHPGGTAPEQVLAAVKAARAAL 467


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: 537
Number of extensions: 19
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: 468
Length adjustment: 33
Effective length of query: 428
Effective length of database: 435
Effective search space:   186180
Effective search space used:   186180
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 BPHYT_RS05210 BPHYT_RS05210 (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.24550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     1e-186  607.3   0.0   1.2e-186  607.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS05210  BPHYT_RS05210 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS05210  BPHYT_RS05210 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.1   0.0  1.2e-186  1.2e-186       2     454 ..      12     467 ..      11     468 .] 0.98

  Alignments for each domain:
  == domain 1  score: 607.1 bits;  conditional E-value: 1.2e-186
                                TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegk 71 
                                              w+ R+++ +++ v+++++s+ fDk+la  Diegs+ah+ +La + i+ +++ + ++++++++k e+++g+
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210  12 WSARFSEPMSELVKRYTSSVFFDKRLALVDIEGSLAHASMLAAQKIIAADDLAAIQRGMAQIKGEIERGE 81 
                                              9********************************************************************* PP

                                TIGR00838  72 lelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekA 141
                                              +e++ d eD+Hl++E++l++ +g d+gk+lhtgrsRnDqvatd+rl+lr +++++   l +l++al++ A
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210  82 FEWQLDLEDVHLNIEARLTALIG-DAGKRLHTGRSRNDQVATDIRLWLRGEIDRIGGLLTELRTALLDMA 150
                                              ***********************.********************************************** PP

                                TIGR00838 142 ekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrella 211
                                              ek+ +t+mpg+tHLq AqP+t++Hhllay+em++rD eR++d  kRvn+ PlG++Alagts++idr+++a
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210 151 EKNASTIMPGFTHLQVAQPVTFGHHLLAYVEMFSRDAERMIDCRKRVNRLPLGAAALAGTSYPIDRHAVA 220
                                              ********************************************************************** PP

                                TIGR00838 212 elLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqK 281
                                              ++LgFd +++nsldavsdRDf+iE+ +a+al+m+h+sr++Eel+l+ s  +gf++l+d++++gssimPqK
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210 221 KTLGFDGICANSLDAVSDRDFAIEFTAASALVMTHVSRFSEELVLWMSPRVGFIDLADRFCTGSSIMPQK 290
                                              ********************************************************************** PP

                                TIGR00838 282 KnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnk 351
                                              KnpDv El+Rgktgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++tv ++l++++ +++ + v+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210 291 KNPDVPELARGKTGRVNGHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTVADTLRIFAEMVAGISVKP 360
                                              ********************************************************************** PP

                                TIGR00838 352 erleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqk....lseklee 417
                                              + +++aa ++f++atdlAdylv++G+PFR+ahe v  +v+ + ++G +l +ltlee++k    + + + e
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210 361 QAMRDAALQGFSTATDLADYLVKRGLPFRDAHEAVALAVRVCADRGCDLADLTLEEMRKelpnVAHLIGE 430
                                              *******************************************************998733335667899 PP

                                TIGR00838 418 dvlevldleeavekrdakGGtakeevekaieeakael 454
                                              dv++ l+le +v+ r+  GGta+e+v  a+++a+a l
  lcl|FitnessBrowser__BFirm:BPHYT_RS05210 431 DVFSYLTLEGSVASRNHPGGTAPEQVLAAVKAARAAL 467
                                              *********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (468 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: 7.85
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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