Alignments for a candidate for ilvA in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Methylobacterium nodulans ORS 2060

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_015931708.1 MNOD_RS24820 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000022085.1:WP_015931708.1
          Length = 515

 Score =  553 bits (1426), Expect = e-162
 Identities = 285/503 (56%), Positives = 371/503 (73%), Gaps = 3/503 (0%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +Y++ VL A VY+ A  +PL +M +LS R+   +L+KRED QPV SFKLRGAY  MAGL+
Sbjct: 3   DYIKKVLTARVYDVAIESPLDRMPRLSGRIGAPVLLKREDLQPVFSFKLRGAYNKMAGLS 62

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134
            E    GVI ASAGNHAQGVA ++A+LG +A IVMP  T  IKV+AVR  GG  +LHG  
Sbjct: 63  REALERGVICASAGNHAQGVALAAAKLGARATIVMPRTTPAIKVEAVRARGGNAVLHGDA 122

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLA 193
           FDEA A A  L  +QG T++ P+D P VIAGQGT+ LE+L Q +  ++ +FVP+GGGGLA
Sbjct: 123 FDEAYAHAKALEAEQGLTFIHPYDDPEVIAGQGTIGLEILHQHSGPIEAIFVPIGGGGLA 182

Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253
           AG+A+++K L P+ KVI VE ED+A + AAL AG  V L  VGLFA+GVAV++ G ETFR
Sbjct: 183 AGIAIVVKFLRPETKVIGVEPEDAAGMAAALKAGERVVLNSVGLFADGVAVRQAGAETFR 242

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIR-GERLAH 312
           LC+EYLD ++TV +DAICAA+KD+F+D RA++EPSGALA+AG+K + A +    G  L  
Sbjct: 243 LCREYLDGVVTVGTDAICAAVKDVFDDTRAISEPSGALAVAGLKAWAAENGAGPGGALVA 302

Query: 313 ILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFA 372
           I SGAN+NF  LR+++ER ELGE+RE L+AVTIPE +GS+  F Q LG R++TEFNYR+A
Sbjct: 303 INSGANLNFDRLRHIAERAELGERREVLIAVTIPERRGSYRAFIQALGQRAITEFNYRYA 362

Query: 373 DAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQ 432
           +  +A IFVGV+L     E++ ++  L + GY V+DLSD+EMAK HVRYMVGGR      
Sbjct: 363 EGPDAHIFVGVQLQGQPGEKRALIASLTEAGYPVLDLSDNEMAKTHVRYMVGGRVPGLTD 422

Query: 433 ERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFETR 491
           ERL+ FEFPE PGALL+FL+ LG  WNISLFHYR+HG DYGR+LA  ++ + +   F+  
Sbjct: 423 ERLFRFEFPERPGALLKFLDGLGDAWNISLFHYRNHGADYGRILAGIQVPESDRTRFQRA 482

Query: 492 LNELGYDCHDETNNPAFRFFLAG 514
           L++LGY  HDE+ NPA+R FL G
Sbjct: 483 LDDLGYPYHDESGNPAYRLFLDG 505


Lambda     K      H
   0.321    0.138    0.403 

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: 759
Number of extensions: 40
Number of successful extensions: 5
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: 514
Length of database: 515
Length adjustment: 35
Effective length of query: 479
Effective length of database: 480
Effective search space:   229920
Effective search space used:   229920
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: 52 (24.6 bits)

Align candidate WP_015931708.1 MNOD_RS24820 (threonine ammonia-lyase, biosynthetic)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

# 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/TIGR01124.hmm
# target sequence database:        /tmp/gapView.15717.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01124  [M=499]
Accession:   TIGR01124
Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-249  813.0   0.0     5e-249  812.9   0.0    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015931708.1  MNOD_RS24820 threonine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015931708.1  MNOD_RS24820 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.9   0.0    5e-249    5e-249       1     499 []       3     503 ..       3     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 812.9 bits;  conditional E-value: 5e-249
                                 TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 
                                               dy++++l+arvy++a+e+pl+++ +ls r++  vllkredlqpvfsfklrGaynkma ls+e+  +Gvi
  lcl|NCBI__GCF_000022085.1:WP_015931708.1   3 DYIKKVLTARVYDVAIESPLDRMPRLSGRIGAPVLLKREDLQPVFSFKLRGAYNKMAGLSREALERGVI 71 
                                               89******************************************************************* PP

                                 TIGR01124  70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekglt 138
                                               +asaGnhaqGval+a+klG +a+ivmp+ttp ikv+av+a+Gg+ vlhG+++dea+a+a++l+ e+glt
  lcl|NCBI__GCF_000022085.1:WP_015931708.1  72 CASAGNHAQGVALAAAKLGARATIVMPRTTPAIKVEAVRARGGNAVLHGDAFDEAYAHAKALEAEQGLT 140
                                               ********************************************************************* PP

                                 TIGR01124 139 fiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207
                                               fi+p+ddp viaGqGt++le+l+q++ +++a+fvp+GGGGl+aG+a++vk l+pe kvigve+ed+a +
  lcl|NCBI__GCF_000022085.1:WP_015931708.1 141 FIHPYDDPEVIAGQGTIGLEILHQHSGPIEAIFVPIGGGGLAAGIAIVVKFLRPETKVIGVEPEDAAGM 209
                                               ********************************************************************* PP

                                 TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaG 276
                                               ++al+aGerv l++vGlfadGvav++ G+etfrlc+eyld +v+v td++caa+kdvf+dtra+ ep+G
  lcl|NCBI__GCF_000022085.1:WP_015931708.1 210 AAALKAGERVVLNSVGLFADGVAVRQAGAETFRLCREYLDGVVTVGTDAICAAVKDVFDDTRAISEPSG 278
                                               ********************************************************************* PP

                                 TIGR01124 277 alalaGlkkyvakkgie.dktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfve 344
                                               ala+aGlk+++a++g+  +  lvai+sGanlnfdrlr+++eraelGe+re l+avtipe++Gs++ f++
  lcl|NCBI__GCF_000022085.1:WP_015931708.1 279 ALAVAGLKAWAAENGAGpGGALVAINSGANLNFDRLRHIAERAELGERREVLIAVTIPERRGSYRAFIQ 347
                                               **************9853899************************************************ PP

                                 TIGR01124 345 vlGeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGr 412
                                                lG+raitefnyr+a+  +ahifvGvql+ +  e++ l+a+l+eagy v+dl+d+e+ak+hvry+vGGr
  lcl|NCBI__GCF_000022085.1:WP_015931708.1 348 ALGQRAITEFNYRYAEGPDAHIFVGVQLQGQpGEKRALIASLTEAGYPVLDLSDNEMAKTHVRYMVGGR 416
                                               ****************************96559************************************ PP

                                 TIGR01124 413 aakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflae 481
                                               +  +++erl++fefperpGallkfl+ l  +wnislfhyrnhGadyGr+l+g++vp+++ ++f+ +l++
  lcl|NCBI__GCF_000022085.1:WP_015931708.1 417 VPGLTDERLFRFEFPERPGALLKFLDGLGDAWNISLFHYRNHGADYGRILAGIQVPESDRTRFQRALDD 485
                                               ********************************************************************* PP

                                 TIGR01124 482 lgyryedetenpayrlfl 499
                                               lgy y+de+ npayrlfl
  lcl|NCBI__GCF_000022085.1:WP_015931708.1 486 LGYPYHDESGNPAYRLFL 503
                                               *****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (515 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.14
//
[ok]

This GapMind analysis is from Apr 10 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