Alignments for a candidate for tdcB in Microvirga lotononidis WSM3557

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Microvirga lotononidis WSM3557

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_085985190.1 MICLODRAFT_RS33510 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000262405.1:WP_085985190.1
          Length = 519

 Score =  568 bits (1465), Expect = e-166
 Identities = 292/506 (57%), Positives = 376/506 (74%), Gaps = 2/506 (0%)

Query: 9   GAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYA 68
           G  +  +Y+R +L APVY+ A  +PL  M +LS RL   + +KRED QPV SFKLRGAYA
Sbjct: 5   GGSDVQDYIRRILSAPVYDVAIESPLDPMPRLSLRLGTPVRLKREDLQPVFSFKLRGAYA 64

Query: 69  MMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEV 128
            MAGL  E    GVI ASAGNHAQGVA ++ +LG KA IVMP  T  IK+ AV+G GG V
Sbjct: 65  RMAGLPREALERGVICASAGNHAQGVAVAAKKLGAKATIVMPRTTPAIKIQAVKGQGGRV 124

Query: 129 LLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPV 187
           +LHG +FDEA + A +L  ++G T++ P+D P VIAGQGT+ +E+L+Q    L+ +FVP+
Sbjct: 125 ILHGESFDEAYSHAQQLEAEKGLTFIHPYDDPDVIAGQGTVGMEILRQHPDPLEAIFVPI 184

Query: 188 GGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRI 247
           GGGGLAAGVAV  K L P++KVI VE ED+A + AAL AG  V L +VGLFA+GVAV++ 
Sbjct: 185 GGGGLAAGVAVYTKFLRPEVKVIGVEPEDAASMAAALAAGDRVILNQVGLFADGVAVRQA 244

Query: 248 GDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRG 307
           G+ETFRLC+E LD++ITV +D ICAA+KD+FED RA+AEPSGA++LAG+KKY+     R 
Sbjct: 245 GEETFRLCRELLDEVITVSTDEICAAVKDIFEDTRAIAEPSGAVSLAGLKKYVEREGARQ 304

Query: 308 ERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEF 367
           + L  + SGAN+NF  LR+++ER ELGE REALLAVTIPE+ GS+ +F QLLG RS+TEF
Sbjct: 305 QGLVAVNSGANMNFDRLRHIAERAELGEHREALLAVTIPEQPGSYRRFIQLLGKRSITEF 364

Query: 368 NYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRP 427
           NYR++D + A IFVGV+LS G  E+++I+ ML + GY V+D+SD+EMAKLHVRYMVGG  
Sbjct: 365 NYRYSDPQEAQIFVGVQLSDGDPEKRQIIAMLREQGYPVLDMSDNEMAKLHVRYMVGGHT 424

Query: 428 SHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-P 486
                E ++ F+FPE PGALL+FLN L   WNISLFHYR+HG DYGRVLA  ++   E  
Sbjct: 425 PGLQDELIFRFQFPERPGALLKFLNGLSGSWNISLFHYRNHGADYGRVLAGIQVPTAERA 484

Query: 487 DFETRLNELGYDCHDETNNPAFRFFL 512
             +  L+ELGY   DE++NPA+R FL
Sbjct: 485 QLKHSLDELGYPYWDESDNPAYRSFL 510


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: 752
Number of extensions: 36
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: 519
Length adjustment: 35
Effective length of query: 479
Effective length of database: 484
Effective search space:   231836
Effective search space used:   231836
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_085985190.1 MICLODRAFT_RS33510 (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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.432229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-252  824.5   0.0   1.6e-252  824.3   0.0    1.0  1  NCBI__GCF_000262405.1:WP_085985190.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000262405.1:WP_085985190.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  824.3   0.0  1.6e-252  1.6e-252       1     499 []      11     510 ..      11     510 .. 1.00

  Alignments for each domain:
  == domain 1  score: 824.3 bits;  conditional E-value: 1.6e-252
                             TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasa 73 
                                           dy+r+il a vy++a+e+pl+++ +ls rl+  v lkredlqpvfsfklrGay++ma l++e+  +Gvi+asa
  NCBI__GCF_000262405.1:WP_085985190.1  11 DYIRRILSAPVYDVAIESPLDPMPRLSLRLGTPVRLKREDLQPVFSFKLRGAYARMAGLPREALERGVICASA 83 
                                           89*********************************************************************** PP

                             TIGR01124  74 GnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddp 146
                                           GnhaqGva++akklG ka+ivmp+ttp ik++avk++Gg+v+lhGe++dea+++a++l+ ekgltfi+p+ddp
  NCBI__GCF_000262405.1:WP_085985190.1  84 GNHAQGVAVAAKKLGAKATIVMPRTTPAIKIQAVKGQGGRVILHGESFDEAYSHAQQLEAEKGLTFIHPYDDP 156
                                           ************************************************************************* PP

                             TIGR01124 147 lviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkl 219
                                           +viaGqGtv++e+lrq+ ++l+a+fvp+GGGGl+aGva++ k l+pe+kvigve+ed+a++++al+aG+rv l
  NCBI__GCF_000262405.1:WP_085985190.1 157 DVIAGQGTVGMEILRQHPDPLEAIFVPIGGGGLAAGVAVYTKFLRPEVKVIGVEPEDAASMAAALAAGDRVIL 229
                                           ************************************************************************* PP

                             TIGR01124 220 dqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgi 292
                                           +qvGlfadGvav++ G+etfrlc+e+ld++++v tde+caa+kd+fedtra++ep+Ga++laGlkkyv+++g+
  NCBI__GCF_000262405.1:WP_085985190.1 230 NQVGLFADGVAVRQAGEETFRLCRELLDEVITVSTDEICAAVKDIFEDTRAIAEPSGAVSLAGLKKYVEREGA 302
                                           ************************************************************************* PP

                             TIGR01124 293 edktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekah 365
                                           +++ lva++sGan+nfdrlr+++eraelGe+reallavtipe++Gs+++f+++lG+r+itefnyr++d ++a+
  NCBI__GCF_000262405.1:WP_085985190.1 303 RQQGLVAVNSGANMNFDRLRHIAERAELGEHREALLAVTIPEQPGSYRRFIQLLGKRSITEFNYRYSDPQEAQ 375
                                           ************************************************************************* PP

                             TIGR01124 366 ifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfl 437
                                           ifvGvql++   e+++++a+l+e+gy v+d++d+e+aklhvry+vGG +  +++e +++f+fperpGallkfl
  NCBI__GCF_000262405.1:WP_085985190.1 376 IFVGVQLSDGdPEKRQIIAMLREQGYPVLDMSDNEMAKLHVRYMVGGHTPGLQDELIFRFQFPERPGALLKFL 448
                                           *******9875799*********************************************************** PP

                             TIGR01124 438 etlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                           + l ++wnislfhyrnhGadyGrvl+g++vp++e +++++ l+elgy y+de++npayr fl
  NCBI__GCF_000262405.1:WP_085985190.1 449 NGLSGSWNISLFHYRNHGADYGRVLAGIQVPTAERAQLKHSLDELGYPYWDESDNPAYRSFL 510
                                           ************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (519 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: 00:00:00.00
# Mc/sec: 28.71
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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

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 catabolism of small carbon sources