GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Nocardioides daejeonensis MJ31

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_110207179.1 DNK54_RS11795 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_003194585.1:WP_110207179.1
          Length = 406

 Score =  403 bits (1036), Expect = e-117
 Identities = 197/392 (50%), Positives = 265/392 (67%), Gaps = 3/392 (0%)

Query: 11  IDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKD 70
           I +   + A+NYHPLP+VI++A GA V D +G  Y+D L+AYSAVN GHR+P++      
Sbjct: 14  IAEVERHAAHNYHPLPVVIADAEGATVVDIDGRRYLDCLAAYSAVNFGHRNPRLTAVAHA 73

Query: 71  QADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGV 130
           Q D++TLTSRAFH+  LGPF    A+L GKEM+LPMNTGAEAVES +K AR+W YEVKGV
Sbjct: 74  QLDRLTLTSRAFHSAALGPFCSALAELAGKEMVLPMNTGAEAVESGIKVARKWGYEVKGV 133

Query: 131 ADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNT 190
           A ++A I+   GNFHGRT   VS S + +   G+GP  PG + +PYGD  A+ +AI  +T
Sbjct: 134 ATDRANIVVAHGNFHGRTTTIVSFSDDPDAFTGYGPFTPGFRSVPYGDAAAVAEAIDDDT 193

Query: 191 AAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIV 250
            A L EPIQGEAG++IPP  +L +   +    +VL I DEIQ+GLGRTG TFACD  G+ 
Sbjct: 194 VAVLLEPIQGEAGVIIPPGDYLPQVRDVTAARDVLLIVDEIQSGLGRTGATFACDLVGVT 253

Query: 251 PDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEK 310
           PD+Y+LGKALGGG+ P+S +  D ++LGV  PG HGSTFGGNPLA AV +A +E+L   +
Sbjct: 254 PDLYLLGKALGGGIVPVSAVVGDADVLGVLRPGQHGSTFGGNPLAAAVGLAVVELLATGE 313

Query: 311 LADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEA---ARPYCERLKEEGLLCK 367
           +  R+  LGE  +  L +     +  VR  GL+ GV++  A   AR  CER+   G+L K
Sbjct: 314 MQLRAKTLGESLREGLTAYLGHGLTAVRSVGLWAGVDVDPAAGTAREVCERMMRGGVLAK 373

Query: 368 ETHDTVIRFAPPLIISKEDLDWAIEKIKHVLR 399
           +TH   +R APPL++++ +LD A+  +   LR
Sbjct: 374 DTHGQTVRLAPPLVVTEAELDRAVAALGSALR 405


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: 461
Number of extensions: 21
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: 406
Length adjustment: 31
Effective length of query: 370
Effective length of database: 375
Effective search space:   138750
Effective search space used:   138750
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_110207179.1 DNK54_RS11795 (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.802402.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-142  461.4   0.0   1.3e-142  461.2   0.0    1.0  1  NCBI__GCF_003194585.1:WP_110207179.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003194585.1:WP_110207179.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.2   0.0  1.3e-142  1.3e-142       4     400 ..      13     403 ..      10     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 461.2 bits;  conditional E-value: 1.3e-142
                             TIGR01885   4 vieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssraf 76 
                                           +i+  e+++ahnyhplpvv++ aeGa+v d++g+ryld l+aysavn Gh  p++ ++   q ++ltl+sraf
  NCBI__GCF_003194585.1:WP_110207179.1  13 AIAEVERHAAHNYHPLPVVIADAEGATVVDIDGRRYLDCLAAYSAVNFGHRNPRLTAVAHAQLDRLTLTSRAF 85 
                                           5677789****************************************************************** PP

                             TIGR01885  77 yndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavisls 149
                                           ++ ++g f   +++l G ++vlpmntGaeave++ik+arkWgy++k++++d+a i++a+gnfhGrt +++s s
  NCBI__GCF_003194585.1:WP_110207179.1  86 HSAALGPFCSALAELAGKEMVLPMNTGAEAVESGIKVARKWGYEVKGVATDRANIVVAHGNFHGRTTTIVSFS 158
                                           ************************************************************************* PP

                             TIGR01885 150 tdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkynvl 222
                                            dp++ +++Gp++p++++++y++++a+ ea+++   + +a+l+ePiqGeaGv++p  +yl +vr++    +vl
  NCBI__GCF_003194585.1:WP_110207179.1 159 DDPDAFTGYGPFTPGFRSVPYGDAAAVAEAIDD---DTVAVLLEPIQGEAGVIIPPGDYLPQVRDVTAARDVL 228
                                           *******************************99...677899******************************* PP

                             TIGR01885 223 liadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPlasav 295
                                           li+deiq G++rtG  +a++  +v Pd+ llGkal+gG++Pvsav++d +v+ +++pg+hGst+gGnPla+av
  NCBI__GCF_003194585.1:WP_110207179.1 229 LIVDEIQSGLGRTGATFACDLVGVTPDLYLLGKALGGGIVPVSAVVGDADVLGVLRPGQHGSTFGGNPLAAAV 301
                                           ************************************************************************* PP

                             TIGR01885 296 avaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivideskangreawdlclklkekGll 368
                                            +a +e+l   ++  ra+ lGe+lre l++   + ++ vr  Gl +++ +d+ +    +a ++c +++  G+l
  NCBI__GCF_003194585.1:WP_110207179.1 302 GLAVVELLATGEMQLRAKTLGESLREGLTAYLGHGLTAVRSVGLWAGVDVDPAA---GTAREVCERMMRGGVL 371
                                           ****************************************************99...8999************ PP

                             TIGR01885 369 akptheeiirlaPPlviteeelkeaveiikkv 400
                                           ak+th++ +rlaPPlv+te el++av  + ++
  NCBI__GCF_003194585.1:WP_110207179.1 372 AKDTHGQTVRLAPPLVVTEAELDRAVAALGSA 403
                                           ************************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (406 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.58
//
[ok]

This GapMind analysis is from Sep 24 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