Alignments for a candidate for argH in Epibacterium ulvae U95

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Epibacterium ulvae U95

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_090214906.1 CV091_RS08375 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_002796795.1:WP_090214906.1
          Length = 464

 Score =  422 bits (1085), Expect = e-122
 Identities = 225/457 (49%), Positives = 296/457 (64%), Gaps = 1/457 (0%)

Query: 5   NHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIK 64
           ++++WGGRF AG    +E   ASI FD+++A  D++GS AH  ML   G+I+  DA  I+
Sbjct: 6   SNQMWGGRFAAGPDAIMEAINASIGFDKRMAAQDIQGSRAHAAMLAASGVITDSDAEAIR 65

Query: 65  AGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLY 124
            GL  +L E +AG  +F  + EDIHMN+E+ L   IG  AG+LHT RSRNDQVATD  L+
Sbjct: 66  EGLLTILSEIEAGNFQFSTALEDIHMNVEARLKEIIGEPAGRLHTGRSRNDQVATDFKLW 125

Query: 125 LKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDS 184
           ++ +LD     L  L   L+D A+     +MPG+THLQ AQP+++GHH+MAY  MF RD 
Sbjct: 126 VRDQLDAAETGLLALIAALLDQAEAGADWVMPGFTHLQTAQPVTWGHHMMAYVEMFGRDL 185

Query: 185 ERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLS 244
            R        +  PLGAAALAGT+FPIDR MTA+ +GF  P +NSLDAVSDRDF LEFLS
Sbjct: 186 SRVRDARTRMNECPLGAAALAGTSFPIDRSMTAEALGFERPAANSLDAVSDRDFALEFLS 245

Query: 245 NASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVY 304
            ASI  +H+SR  EE++ W S +++FVTLSD FSTGSSIMPQKKNPD AELIR K GR++
Sbjct: 246 VASICAVHLSRFAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRAKVGRIF 305

Query: 305 ANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAEST 364
                L+ VMK LPLAY+KD+QEDKE +FD A+ + +AL  + GM+  M  N + +A + 
Sbjct: 306 GANTALMMVMKGLPLAYSKDMQEDKEQVFDAADNLMLALAAMEGMVKDMSANRESLAAAA 365

Query: 365 QKDFSNATELADYLAS-KGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEE 423
              FS AT+LAD+L     +PFR AH + G L+      G  L D+ L+  Q +   I E
Sbjct: 366 GSGFSTATDLADWLVRVLKVPFRDAHHVTGTLVGMAEARGCDLPDLSLDDMQGVHSGITE 425

Query: 424 DVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
           D++  L    +V  R S GGT  EQV+ Q+   K  L
Sbjct: 426 DIFTVLGVENSVNSRTSYGGTAPEQVRAQVTRWKALL 462


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: 546
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: 460
Length of database: 464
Length adjustment: 33
Effective length of query: 427
Effective length of database: 431
Effective search space:   184037
Effective search space used:   184037
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_090214906.1 CV091_RS08375 (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.2797898.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-185  602.2   0.0     4e-185  602.0   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090214906.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090214906.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.0   0.0    4e-185    4e-185       1     453 [.       9     461 ..       9     463 .. 0.99

  Alignments for each domain:
  == domain 1  score: 602.0 bits;  conditional E-value: 4e-185
                             TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 
                                           +wggR++ ++d  +++ nas+ fDk++a++Di+gs ah+++La  g++t+ +a+ ++e+L ++ +e+++g+++
  NCBI__GCF_002796795.1:WP_090214906.1   9 MWGGRFAAGPDAIMEAINASIGFDKRMAAQDIQGSRAHAAMLAASGVITDSDAEAIREGLLTILSEIEAGNFQ 81 
                                           6************************************************************************ PP

                             TIGR00838  74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146
                                           +++  eDiH++vE++l + +ge +g +lhtgrsRnDqvatd++l++rd+++   + l++l++al+++Ae+  +
  NCBI__GCF_002796795.1:WP_090214906.1  82 FSTALEDIHMNVEARLKEIIGEPAG-RLHTGRSRNDQVATDFKLWVRDQLDAAETGLLALIAALLDQAEAGAD 153
                                           *********************7766.*********************************************** PP

                             TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219
                                            +mpg+tHLq AqP+t++Hh++ay+em+ rDl+R+ da  R+n++PlG++Alagtsf+idr+++ae LgF++ 
  NCBI__GCF_002796795.1:WP_090214906.1 154 WVMPGFTHLQTAQPVTWGHHMMAYVEMFGRDLSRVRDARTRMNECPLGAAALAGTSFPIDRSMTAEALGFERP 226
                                           ************************************************************************* PP

                             TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292
                                           ++nsldavsdRDf++E+ls+a++++vhlsr+aEel+++ss+ f fv+lsd++s+gssimPqKKnpD+aEliR+
  NCBI__GCF_002796795.1:WP_090214906.1 227 AANSLDAVSDRDFALEFLSVASICAVHLSRFAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRA 299
                                           ************************************************************************* PP

                             TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365
                                           k gr++G  t+l++++K+lPlaY kD+qEdke++fda +++  +l +++g++k++  n+e l+ aa ++f++a
  NCBI__GCF_002796795.1:WP_090214906.1 300 KVGRIFGANTALMMVMKGLPLAYSKDMQEDKEQVFDAADNLMLALAAMEGMVKDMSANRESLAAAAGSGFSTA 372
                                           ************************************************************************* PP

                             TIGR00838 366 tdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437
                                           tdlAd+lvr   vPFR+ah+++G +v  a+++G +l +l+l+ +q +++ ++ed+++vl +e++v+ r+++GG
  NCBI__GCF_002796795.1:WP_090214906.1 373 TDLADWLVRVlKVPFRDAHHVTGTLVGMAEARGCDLPDLSLDDMQGVHSGITEDIFTVLGVENSVNSRTSYGG 445
                                           *********99************************************************************** PP

                             TIGR00838 438 takeevekaieeakae 453
                                           ta+e+v+ ++   ka 
  NCBI__GCF_002796795.1:WP_090214906.1 446 TAPEQVRAQVTRWKAL 461
                                           **********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (464 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.57
//
[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:

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 2024 update 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 original 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