GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Sinorhizobium fredii NGR234

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_012709571.1 NGR_RS26550 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000018545.1:WP_012709571.1
          Length = 401

 Score =  440 bits (1131), Expect = e-128
 Identities = 212/397 (53%), Positives = 282/397 (71%), Gaps = 4/397 (1%)

Query: 6   KSKEIIDQTSHY-GANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKI 64
           K+   + +T H  GA+NY PL +V++   G +V D EGN Y+D LSAYSAVNQGH HPKI
Sbjct: 2   KTTAALIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKI 61

Query: 65  IQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWA 124
            +A+ +QA K+TLTSRAF NDQL  FYE+ A LTG   +LPMN+GAEAVE+A+KA R+W 
Sbjct: 62  FKAMVEQAQKLTLTSRAFRNDQLALFYEEIAALTGSHKVLPMNSGAEAVETAIKAVRKWG 121

Query: 125 YEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQ 184
           YEVKGVA +QAEII C  NFHGRT+  V  S++ +   GFGP  PG +++P+GD++A R 
Sbjct: 122 YEVKGVAADQAEIIVCANNFHGRTIGIVGFSTDPDSHDGFGPFAPGFRIVPFGDIDAFRA 181

Query: 185 AITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFAC 244
           AI+ NT AFL EPIQGEAG+++PP G+  E   +C +  +  + DEIQTGLGRTGK  A 
Sbjct: 182 AISENTVAFLVEPIQGEAGVIVPPAGYFAEVRELCTKHAITLVLDEIQTGLGRTGKLLAE 241

Query: 245 DWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLE 304
           + + I  D+ ++GKAL GG +P+S + ++ E+LGV  PG HGSTFGGNPLACA++ A+L+
Sbjct: 242 EHEAIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAIARAALK 301

Query: 305 VLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTE---AARPYCERLKE 361
           VL +E + + S  +GE F + L  I S +I+EVRGRGL + VEL      AR YCE LK 
Sbjct: 302 VLTEEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVPEAGGARKYCEALKA 361

Query: 362 EGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398
            G+L K+TH   IR APPL+I+  ++DWA+E+   VL
Sbjct: 362 RGILAKDTHGDTIRIAPPLVITAGEVDWALEQFAAVL 398


Lambda     K      H
   0.318    0.136    0.401 

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: 468
Number of extensions: 13
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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: 50 (23.9 bits)

Align candidate WP_012709571.1 NGR_RS26550 (ornithine--oxo-acid transaminase)
to HMM TIGR01885 (rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13))

# 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/TIGR01885.hmm
# target sequence database:        /tmp/gapView.2745220.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01885  [M=402]
Accession:   TIGR01885
Description: Orn_aminotrans: ornithine--oxo-acid transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-169  549.6   0.0   2.2e-169  549.3   0.0    1.0  1  NCBI__GCF_000018545.1:WP_012709571.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012709571.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.3   0.0  2.2e-169  2.2e-169       3     400 ..       6     397 ..       4     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 549.3 bits;  conditional E-value: 2.2e-169
                             TIGR01885   3 evieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssra 75 
                                           ++ie+e+  gahny+pl+vvl+++eG++vwd+eg+ryld lsaysavnqGhchpki ka+veqaqkltl+sra
  NCBI__GCF_000018545.1:WP_012709571.1   6 ALIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKIFKAMVEQAQKLTLTSRA 78 
                                           6899********************************************************************* PP

                             TIGR01885  76 fyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavisl 148
                                           f nd+++ f e ++ l G  kvlpmn+Gaeavetaik +rkWgy++k++++d+a i+++++nfhGrt++++  
  NCBI__GCF_000018545.1:WP_012709571.1  79 FRNDQLALFYEEIAALTGSHKVLPMNSGAEAVETAIKAVRKWGYEVKGVAADQAEIIVCANNFHGRTIGIVGF 151
                                           ************************************************************************* PP

                             TIGR01885 149 stdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkynv 221
                                           stdp+s+++fGp++p+++ +++++++a++ a++e   + +aflvePiqGeaGv+vp  gy+ +vrelc+k+ +
  NCBI__GCF_000018545.1:WP_012709571.1 152 STDPDSHDGFGPFAPGFRIVPFGDIDAFRAAISE---NTVAFLVEPIQGEAGVIVPPAGYFAEVRELCTKHAI 221
                                           *******************************998...899********************************* PP

                             TIGR01885 222 lliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPlasa 294
                                            l+ deiqtG++rtGklla ehe +  d+ l+GkalsgG+yPvsavl+++ev+ ++kpg+hGst+gGnPla+a
  NCBI__GCF_000018545.1:WP_012709571.1 222 TLVLDEIQTGLGRTGKLLAEEHEAIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACA 294
                                           ************************************************************************* PP

                             TIGR01885 295 vavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivideskangreawdlclklkekGl 367
                                           +a aal+vl+ee ++e+++++Ge++ + l++++++i++evrG+Gl+ a+ + +++     a + c  lk +G+
  NCBI__GCF_000018545.1:WP_012709571.1 295 IARAALKVLTEEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVPEA---GGARKYCEALKARGI 364
                                           ****************************************************999...677889********* PP

                             TIGR01885 368 lakptheeiirlaPPlviteeelkeaveiikkv 400
                                           lak+th++ ir+aPPlvit  e+++a+e ++ v
  NCBI__GCF_000018545.1:WP_012709571.1 365 LAKDTHGDTIRIAPPLVITAGEVDWALEQFAAV 397
                                           **************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (401 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: 00:00:00.00
# Mc/sec: 21.95
//
[ok]

This GapMind analysis is from Apr 09 2024. 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