GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Shewanella amazonensis SB2B

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 6939184 Sama_3278 threonine dehydratase (RefSeq)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__SB2B:6939184
          Length = 531

 Score =  604 bits (1557), Expect = e-177
 Identities = 308/506 (60%), Positives = 382/506 (75%), Gaps = 10/506 (1%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           YL+ +L + VY+ A+VTPL  M KLS+RL   I +KRED QPVHSFKLRGAY  ++ LT+
Sbjct: 24  YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQ 83

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
            +   GV+ ASAGNHAQGVA S++  G+ A+IVMPT T DIK+DAVR  GG VLLHG +F
Sbjct: 84  PECERGVVCASAGNHAQGVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESF 143

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAG 195
           D+A A A  L+Q +G  ++ PFD   VIAGQGT+A E+LQQ   L+ VFVPVGGGGL AG
Sbjct: 144 DQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTVAQEMLQQQRDLELVFVPVGGGGLVAG 203

Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255
           +A   K + P +K+I VE ED+ACLKAA+ AG PV L +VGLFA+GVAVKRIG E FR+ 
Sbjct: 204 IAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVKRIGAEPFRIA 263

Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIR-------GE 308
           + Y+D+++TV SD ICAA+KD+FED RA+AEP+GAL+LAG+KKY+A              
Sbjct: 264 KHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTTPALAEAGKPAR 323

Query: 309 RLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFN 368
           ++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE  GSFLKFC+LLG R++TEFN
Sbjct: 324 KVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFN 383

Query: 369 YRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPS 428
           YRF+   +A +F G+RLS G  E KEI+  L  GG+ V DLS DE AKLHVRYMVGG P+
Sbjct: 384 YRFSGRDSAVVFAGIRLSGGQSELKEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGHPT 443

Query: 429 HPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL--GDHEP 486
            PL ERL+SFEFPE PGALL+FL TLG+ WNISLFHYR+HG  +GRVLA FE+  GD+E 
Sbjct: 444 EPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHGAAFGRVLAGFEVPEGDNEA 503

Query: 487 DFETRLNELGYDCHDETNNPAFRFFL 512
            F   L ELG+   +ET++PA+R FL
Sbjct: 504 -FGRFLTELGFVWQEETHSPAYRLFL 528


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: 746
Number of extensions: 30
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: 531
Length adjustment: 35
Effective length of query: 479
Effective length of database: 496
Effective search space:   237584
Effective search space used:   237584
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 6939184 Sama_3278 (threonine dehydratase (RefSeq))
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.9074.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-235  768.3   0.0   1.9e-235  768.1   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6939184  Sama_3278 threonine dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939184  Sama_3278 threonine dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.1   0.0  1.9e-235  1.9e-235       2     499 .]      24     528 ..      23     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 768.1 bits;  conditional E-value: 1.9e-235
                         TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaq 78 
                                       yl++il ++vy++a++tpl+++ kls+rl+ +++lkred+qpv+sfklrGayn+++ql++ +  +Gv++asaGnhaq
  lcl|FitnessBrowser__SB2B:6939184  24 YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQPECERGVVCASAGNHAQ 100
                                       89*************************************************************************** PP

                         TIGR01124  79 GvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtv 155
                                       Gvalsa+  G+ avivmp+ttp+ik+dav+ +Gg+v+lhGe++d+a+a+a++laq +g  +iapfdd+ viaGqGtv
  lcl|FitnessBrowser__SB2B:6939184 101 GVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESFDQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTV 177
                                       ***************************************************************************** PP

                         TIGR01124 156 alellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavk 232
                                       a e+l+q++ dl+ vfvpvGGGGl+aG+aa+ k+++p +k+igve+ed+a+lk+a++aGe+v+l+qvGlfadGvavk
  lcl|FitnessBrowser__SB2B:6939184 178 AQEMLQQQR-DLELVFVPVGGGGLVAGIAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVK 253
                                       *******99.9****************************************************************** PP

                         TIGR01124 233 evGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakk.......giedktlvails 302
                                       ++G+e fr++k+y+d++v+v +de+caa+kd+fedtra++epaGal+laGlkky+a+        g   ++++ails
  lcl|FitnessBrowser__SB2B:6939184 254 RIGAEPFRIAKHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTtpalaeaGKPARKVAAILS 330
                                       ******************************************************98752222111455789****** PP

                         TIGR01124 303 GanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eer 378
                                       Gan+nf++lryvser+elGeq+ea+lav +pe +Gs+lkf+e+lG+ra+tefnyr++ +++a +f G++l+   +e 
  lcl|FitnessBrowser__SB2B:6939184 331 GANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFNYRFSGRDSAVVFAGIRLSGGqSEL 407
                                       **********************************************************************9864899 PP

                         TIGR01124 379 kellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhG 455
                                       ke++a+l++ g++v dl+ de aklhvry+vGG +++   erl+sfefpe pGallkfl+tl ++wnislfhyrnhG
  lcl|FitnessBrowser__SB2B:6939184 408 KEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGHPTEPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHG 484
                                       ***************************************************************************** PP

                         TIGR01124 456 adyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                       a++Grvl+g+evp+ ++e+f  fl elg+  ++et++payrlfl
  lcl|FitnessBrowser__SB2B:6939184 485 AAFGRVLAGFEVPEGDNEAFGRFLTELGFVWQEETHSPAYRLFL 528
                                       *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (531 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 9.29
//
[ok]

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

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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