GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Phyllobacterium endophyticum PEPV15

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_106719047.1 CU100_RS23360 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_003010935.1:WP_106719047.1
          Length = 466

 Score =  432 bits (1111), Expect = e-125
 Identities = 228/457 (49%), Positives = 302/457 (66%), Gaps = 1/457 (0%)

Query: 5   NHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIK 64
           ++++WGGRF +G A  +EE  ASI FDQKL   D++GS+AH  ML + GIIS +D   I 
Sbjct: 7   SNEMWGGRFASGPAAIMEEINASIGFDQKLYAQDIQGSLAHAAMLAKTGIISGDDHDKIA 66

Query: 65  AGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLY 124
            GL  +L E + G+  F    EDIHMN+ES L   IG  AG+LHTARSRNDQVA D  L+
Sbjct: 67  KGLNTILSEIETGKFIFSRKLEDIHMNIESRLAELIGAPAGRLHTARSRNDQVAVDFRLW 126

Query: 125 LKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDS 184
           +KA+ ++    L  L    +  A +H  T+MPG+THLQ AQP++FGHH MAY  MF RD 
Sbjct: 127 VKAEFEKTAIALKMLIEAFLKRAAEHATTLMPGFTHLQTAQPVTFGHHCMAYVEMFGRDL 186

Query: 185 ERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLS 244
            R    ++  D SPLGAAALAGT FPIDR MTA+ +GF EP  NSLD+VSDRD+ LEFLS
Sbjct: 187 SRVRDAIERMDESPLGAAALAGTGFPIDRHMTAKALGFREPTRNSLDSVSDRDYALEFLS 246

Query: 245 NASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVY 304
            A+I   H+SR+ EE++ W + ++ FV LSD+FSTGSSIMPQKKNPD AEL+R K+GR+ 
Sbjct: 247 TAAITATHLSRLAEEIVIWSTPQFGFVRLSDSFSTGSSIMPQKKNPDAAELVRAKTGRIT 306

Query: 305 ANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAEST 364
            +L GLLTVMK LPL Y+KD+QEDKE +FD AET+ +A+  + GM+  M +N   M ++ 
Sbjct: 307 GSLVGLLTVMKGLPLTYSKDMQEDKEAVFDAAETLELAIAAMTGMVGDMTINTAAMKKAA 366

Query: 365 QKDFSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEE 423
              +S AT+LAD+L  + G+PFR+AH + G+ +    +    L  + LE  Q I   I +
Sbjct: 367 GSGYSTATDLADWLVRELGLPFREAHHVTGRAVALAERQKVDLGKLALEDMQAIHPGITD 426

Query: 424 DVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
            V+  L    +V  R S GGT   +V+ QI   +K L
Sbjct: 427 AVFGYLTIDKSVRSRKSYGGTAPGEVRRQIRFWQKRL 463


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: 578
Number of extensions: 27
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: 466
Length adjustment: 33
Effective length of query: 427
Effective length of database: 433
Effective search space:   184891
Effective search space used:   184891
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_106719047.1 CU100_RS23360 (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.980818.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-187  608.2   0.0     6e-187  608.1   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106719047.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106719047.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  608.1   0.0    6e-187    6e-187       1     454 [.      10     463 ..      10     464 .. 0.99

  Alignments for each domain:
  == domain 1  score: 608.1 bits;  conditional E-value: 6e-187
                             TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 
                                           +wggR+++++   ++e nas+ fD++l+++Di+gs+ah+++Lak+gi++ ++++k+ ++L+++ +e++ gk+ 
  NCBI__GCF_003010935.1:WP_106719047.1  10 MWGGRFASGPAAIMEEINASIGFDQKLYAQDIQGSLAHAAMLAKTGIISGDDHDKIAKGLNTILSEIETGKFI 82 
                                           6************************************************************************ PP

                             TIGR00838  74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146
                                           ++ + eDiH+++E++l + +g  +g +lht+rsRnDqva+d+rl+++++ ++ a alk l++a++++A+++  
  NCBI__GCF_003010935.1:WP_106719047.1  83 FSRKLEDIHMNIESRLAELIGAPAG-RLHTARSRNDQVAVDFRLWVKAEFEKTAIALKMLIEAFLKRAAEHAT 154
                                           *********************7777.*********************************************** PP

                             TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219
                                           tlmpg+tHLq AqP+t++Hh++ay+em+ rDl+R+ da++R+++sPlG++Alagt+f+idr+++a+ LgF + 
  NCBI__GCF_003010935.1:WP_106719047.1 155 TLMPGFTHLQTAQPVTFGHHCMAYVEMFGRDLSRVRDAIERMDESPLGAAALAGTGFPIDRHMTAKALGFREP 227
                                           ************************************************************************* PP

                             TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292
                                           ++nsld+vsdRD+++E+ls+aa++++hlsrlaEe++++s+  fgfv lsd++s+gssimPqKKnpD+aEl+R+
  NCBI__GCF_003010935.1:WP_106719047.1 228 TRNSLDSVSDRDYALEFLSTAAITATHLSRLAEEIVIWSTPQFGFVRLSDSFSTGSSIMPQKKNPDAAELVRA 300
                                           ************************************************************************* PP

                             TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365
                                           ktgr++G+l+gllt++K+lPl+Y kD+qEdkea+fda +t+e ++ ++tg++ ++++n+  +++aa +++++a
  NCBI__GCF_003010935.1:WP_106719047.1 301 KTGRITGSLVGLLTVMKGLPLTYSKDMQEDKEAVFDAAETLELAIAAMTGMVGDMTINTAAMKKAAGSGYSTA 373
                                           ************************************************************************* PP

                             TIGR00838 366 tdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437
                                           tdlAd+lvr+ G+PFReah+++G++va a+++ ++l +l+le +q++++ +++ v+  l++ ++v+ r+++GG
  NCBI__GCF_003010935.1:WP_106719047.1 374 TDLADWLVRElGLPFREAHHVTGRAVALAERQKVDLGKLALEDMQAIHPGITDAVFGYLTIDKSVRSRKSYGG 446
                                           ********************************99*************************************** PP

                             TIGR00838 438 takeevekaieeakael 454
                                           ta+ ev+++i   +++l
  NCBI__GCF_003010935.1:WP_106719047.1 447 TAPGEVRRQIRFWQKRL 463
                                           **********9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (466 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: 00:00:00.01
# Mc/sec: 17.27
//
[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