Alignments for a candidate for argH in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Sphingomonas koreensis DSMZ 15582

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate Ga0059261_2049 Ga0059261_2049 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__Korea:Ga0059261_2049
          Length = 456

 Score =  405 bits (1041), Expect = e-117
 Identities = 212/453 (46%), Positives = 290/453 (64%), Gaps = 1/453 (0%)

Query: 8   LWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAGL 67
           +WGGRF  G +  + E  ASI FD+++   D+ GS AHV MLGE+GI+   DAATI AGL
Sbjct: 1   MWGGRFAEGPSSVMREINASIPFDKRMWRQDIAGSKAHVAMLGEQGIVDAADAATISAGL 60

Query: 68  EDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLKA 127
           + +  +Y+   +  D++ EDIHM  E+ L  KIGPVAG+LHTARSRNDQVATD  L+++ 
Sbjct: 61  DAVAADYERDGVPEDLALEDIHMLTEARLAEKIGPVAGRLHTARSRNDQVATDFRLWVRD 120

Query: 128 KLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSERF 187
             D+V+  LA L+  L+  AD+H  ++MPG+THLQ AQP++ GHHLMAY+ M  RD  RF
Sbjct: 121 ATDQVLAALAALQDALLARADEHAGSVMPGFTHLQSAQPVTLGHHLMAYFEMIARDVSRF 180

Query: 188 IFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNAS 247
                  +  PLG+AALAGT FP+DR+ TA  +GF  P  NSLDAVSDRDF L++L  A+
Sbjct: 181 ADARARGNRCPLGSAALAGTGFPLDRDATAAALGFDGPTRNSLDAVSDRDFALDYLMAAA 240

Query: 248 ILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYANL 307
              +H+SR+ EE + W S  + FV LSD +STGSSIMPQK+NPD AEL+RG SGR+   L
Sbjct: 241 QCALHLSRLAEEFVIWASQPFGFVKLSDQWSTGSSIMPQKRNPDAAELVRGHSGRIVGCL 300

Query: 308 FGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQKD 367
             L+  MK LPLAY+KD+Q+DK  +F+  + + +++  + GM+ S       M    +  
Sbjct: 301 TSLMITMKGLPLAYSKDMQDDKPPVFEAHDLLALSIAAMTGMVESAQFRTDRMRGLAESG 360

Query: 368 FSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVY 426
           F+ AT+LAD+L  + G+PFR+AH I G+ +         L  + L   Q I   I+E V+
Sbjct: 361 FATATDLADWLVREGGIPFREAHHITGRAVAAAEAKNVRLDQLELADLQAIDQRIDERVF 420

Query: 427 ETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKA 459
             L    +V  R S GGT   +V+  IA A+ A
Sbjct: 421 GVLTVDASVASRISFGGTAPVRVREAIAAARAA 453


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: 569
Number of extensions: 19
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: 460
Length of database: 456
Length adjustment: 33
Effective length of query: 427
Effective length of database: 423
Effective search space:   180621
Effective search space used:   180621
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 Ga0059261_2049 Ga0059261_2049 (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.1619.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-178  580.1   0.0   2.3e-178  579.8   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2049  Ga0059261_2049 argininosuccinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2049  Ga0059261_2049 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.8   0.0  2.3e-178  2.3e-178       1     452 [.       1     452 [.       1     454 [. 0.99

  Alignments for each domain:
  == domain 1  score: 579.8 bits;  conditional E-value: 2.3e-178
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               +wggR+++++++ ++e nas+ fDk++ ++Di gs+ah+++L ++gi+ + +a+ + ++L+ ++ ++++
  lcl|FitnessBrowser__Korea:Ga0059261_2049   1 MWGGRFAEGPSSVMREINASIPFDKRMWRQDIAGSKAHVAMLGEQGIVDAADAATISAGLDAVAADYER 69 
                                               6******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               + + ++   eDiH+  E++l +k+g  v+++lht+rsRnDqvatd+rl++rd+ ++++ al +l++al+
  lcl|FitnessBrowser__Korea:Ga0059261_2049  70 DGVPEDLALEDIHMLTEARLAEKIG-PVAGRLHTARSRNDQVATDFRLWVRDATDQVLAALAALQDALL 137
                                               *************************.9999*************************************** PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                                +A+++   +mpg+tHLq+AqP+tl+Hhl+ay+em++rD++R+ da  R n++PlGs+Alagt+f++dr
  lcl|FitnessBrowser__Korea:Ga0059261_2049 138 ARADEHAGSVMPGFTHLQSAQPVTLGHHLMAYFEMIARDVSRFADARARGNRCPLGSAALAGTGFPLDR 206
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               +++a+ LgFd  ++nsldavsdRDf+++ l+aaa +++hlsrlaEe+++++s+ fgfv+lsd++s+gss
  lcl|FitnessBrowser__Korea:Ga0059261_2049 207 DATAAALGFDGPTRNSLDAVSDRDFALDYLMAAAQCALHLSRLAEEFVIWASQPFGFVKLSDQWSTGSS 275
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqK+npD+aEl+Rg++gr++G lt+l++++K+lPlaY kD+q+dk+++f+a + +  ++ ++tg+++
  lcl|FitnessBrowser__Korea:Ga0059261_2049 276 IMPQKRNPDAAELVRGHSGRIVGCLTSLMITMKGLPLAYSKDMQDDKPPVFEAHDLLALSIAAMTGMVE 344
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklse 413
                                               + +++++r++ +a+++fa+atdlAd+lvr+ G+PFReah+i+G++va+a++k ++l++l l+ lq++++
  lcl|FitnessBrowser__Korea:Ga0059261_2049 345 SAQFRTDRMRGLAESGFATATDLADWLVREgGIPFREAHHITGRAVAAAEAKNVRLDQLELADLQAIDQ 413
                                               ******************************9************************************** PP

                                 TIGR00838 414 kleedvlevldleeavekrdakGGtakeevekaieeaka 452
                                               +++e v+ vl++  +v+ r + GGta+ +v++ai++a+a
  lcl|FitnessBrowser__Korea:Ga0059261_2049 414 RIDERVFGVLTVDASVASRISFGGTAPVRVREAIAAARA 452
                                               ***********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (456 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: 00:00:00.02
# Mc/sec: 10.10
//
[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