GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Sphingomonas indica Dd16

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_085218001.1 B9N75_RS06120 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_900177405.1:WP_085218001.1
          Length = 458

 Score =  407 bits (1047), Expect = e-118
 Identities = 212/454 (46%), Positives = 294/454 (64%), Gaps = 1/454 (0%)

Query: 8   LWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAGL 67
           +WGGRF  G +  + E  ASI FD++L   D+ GS AHV ML  +GI++  DA  I  GL
Sbjct: 1   MWGGRFADGPSAVMREINASIPFDKRLWRQDIAGSKAHVAMLAAQGIVAAADAGAIAKGL 60

Query: 68  EDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLKA 127
           + +  EY+A  +  D++ EDIHM++E  L   IGP AG+LHTARSRNDQVATD  L+++ 
Sbjct: 61  DAIAAEYEADGVAEDLALEDIHMHVEHRLAELIGPAAGRLHTARSRNDQVATDFRLWVRD 120

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

Query: 188 IFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNAS 247
                  +  PLGAAALAGT+FPIDR  TA  +GF  P +NSLD+VSDRDF L++L+ A+
Sbjct: 181 ADARARLNRCPLGAAALAGTSFPIDRAATAAALGFDGPTANSLDSVSDRDFALDYLTAAA 240

Query: 248 ILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYANL 307
              +H+SR+ EE I W S  + FV L D +STGSSIMPQK+NPD AEL+RG +GR+   +
Sbjct: 241 QCALHLSRLAEEFILWASQPFGFVALPDAYSTGSSIMPQKRNPDAAELVRGHAGRIVGAM 300

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

Query: 368 FSNATELADYLAS-KGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVY 426
            + AT+LAD+L    G+PFR+AH I G ++    + G  L D+PL+ +Q I   I+  V+
Sbjct: 361 HATATDLADWLVRVAGIPFREAHHITGGVVKAADEAGLPLWDMPLDAFQAIDPRIDASVF 420

Query: 427 ETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
           + L    +V+ R S GGT  +QV+ +IAEAK AL
Sbjct: 421 DVLSIEASVKSRTSFGGTAPDQVRARIAEAKAAL 454


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: 585
Number of extensions: 20
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: 458
Length adjustment: 33
Effective length of query: 427
Effective length of database: 425
Effective search space:   181475
Effective search space used:   181475
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 WP_085218001.1 B9N75_RS06120 (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.739008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     9e-179  581.1   0.0     1e-178  580.9   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085218001.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085218001.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.9   0.0    1e-178    1e-178       1     454 [.       1     454 [.       1     455 [. 0.99

  Alignments for each domain:
  == domain 1  score: 580.9 bits;  conditional E-value: 1e-178
                             TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 
                                           +wggR++++++  ++e nas+ fDk+l ++Di gs+ah+++La +gi+ + +a  + ++L+ ++ e++++ + 
  NCBI__GCF_900177405.1:WP_085218001.1   1 MWGGRFADGPSAVMREINASIPFDKRLWRQDIAGSKAHVAMLAAQGIVAAADAGAIAKGLDAIAAEYEADGVA 73 
                                           6************************************************************************ PP

                             TIGR00838  74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146
                                           ++   eDiH+ vE++l + +g  ++++lht+rsRnDqvatd+rl++rd+++ +   l ++++al+++A+++ +
  NCBI__GCF_900177405.1:WP_085218001.1  74 EDLALEDIHMHVEHRLAELIG-PAAGRLHTARSRNDQVATDFRLWVRDAIDAVDAGLAAFQRALLDRAAEHAD 145
                                           *********************.7778*********************************************** PP

                             TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219
                                           t+mpg+tHLq AqP+tl+Hhl+ay+ m +rD +R+ da  R+n++PlG++Alagtsf+idr ++a+ LgFd  
  NCBI__GCF_900177405.1:WP_085218001.1 146 TVMPGFTHLQVAQPVTLGHHLMAYHAMADRDRSRFADARARLNRCPLGAAALAGTSFPIDRAATAAALGFDGP 218
                                           ************************************************************************* PP

                             TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292
                                           ++nsld+vsdRDf+++ l+aaa +++hlsrlaEe+il++s+ fgfv l+d++s+gssimPqK+npD+aEl+Rg
  NCBI__GCF_900177405.1:WP_085218001.1 219 TANSLDSVSDRDFALDYLTAAAQCALHLSRLAEEFILWASQPFGFVALPDAYSTGSSIMPQKRNPDAAELVRG 291
                                           ************************************************************************* PP

                             TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365
                                           ++gr++G +t+l++++K+lPlaY kD+q+dk++lf+a + +  ++ ++tg++++  +  +r++ a ++++a+a
  NCBI__GCF_900177405.1:WP_085218001.1 292 HAGRIVGAMTSLMITMKGLPLAYSKDMQDDKPPLFEAHDLLALSIAAMTGMVESAAFVPDRMRAALTAGHATA 364
                                           ************************************************************************* PP

                             TIGR00838 366 tdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437
                                           tdlAd+lvr  G+PFReah+i+G vv++a e+G+ l +++l+ +q+++++++  v++vl++e +v+ r++ GG
  NCBI__GCF_900177405.1:WP_085218001.1 365 TDLADWLVRVaGIPFREAHHITGGVVKAADEAGLPLWDMPLDAFQAIDPRIDASVFDVLSIEASVKSRTSFGG 437
                                           *********99************************************************************** PP

                             TIGR00838 438 takeevekaieeakael 454
                                           ta+++v+ +i+eaka l
  NCBI__GCF_900177405.1:WP_085218001.1 438 TAPDQVRARIAEAKAAL 454
                                           **************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (458 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: 00:00:00.01
# Mc/sec: 17.55
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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