Alignments for a candidate for rocD in Croceitalea dokdonensis DOKDO 023

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocD in Croceitalea dokdonensis DOKDO 023

Align Ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_054559146.1 I595_RS09190 ornithine--oxo-acid transaminase

Query= reanno::Cola:Echvi_0577
         (413 letters)



>NCBI__GCF_001306415.1:WP_054559146.1
          Length = 425

 Score =  582 bits (1499), Expect = e-171
 Identities = 289/424 (68%), Positives = 350/424 (82%), Gaps = 14/424 (3%)

Query: 1   MMQPITSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGH 60
           ++Q ITS Q+AI+LENK+GA NYHPLPVVLSRGEGVF+WDVEG+KYYDFLS+YSAVNQGH
Sbjct: 3   VLQHITS-QEAIDLENKYGAQNYHPLPVVLSRGEGVFVWDVEGKKYYDFLSAYSAVNQGH 61

Query: 61  CHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKI 120
           CHP+I+  L +QA  LTLTSRAF+ND+LG +EKF TE+FG+DK+LPMNTGAE VETA+K+
Sbjct: 62  CHPKIINALKNQAENLTLTSRAFYNDMLGKYEKFATEFFGFDKLLPMNTGAEAVETALKL 121

Query: 121 ARKWGYEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDI 180
           ARKWGYEKKGIP N+  IIV +NNFHGRT ++IS SND  A +NFGP+TPG ++I ++DI
Sbjct: 122 ARKWGYEKKGIPANKAKIIVCQNNFHGRTISIISASNDPVATENFGPFTPGMLSIRYNDI 181

Query: 181 DALKDVLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIAR 240
            AL + L + +++  ++VEPIQGEAGVYVP E Y+KE   +CK   VLF+ADE+QTGIAR
Sbjct: 182 AALAEAL-KDEHVAAFMVEPIQGEAGVYVPDENYIKEAFELCKSKNVLFIADEVQTGIAR 240

Query: 241 TGKLLA------CDHEG------VKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQH 288
           TG+LLA      C  +       VKPD+LILGKAISGG +PVSAVLA++ IMEVI+PG H
Sbjct: 241 TGRLLASCGNCSCSDKNCSGVPDVKPDVLILGKAISGGVFPVSAVLANNDIMEVIRPGNH 300

Query: 289 GSTFGGNPLGAKVAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLL 348
           GSTFGGNPL   VA+ AL VVK+E LAENA +LG+LFR  +Q+LV ++DLV LVRGKGLL
Sbjct: 301 GSTFGGNPLACAVAIAALEVVKEENLAENAFQLGELFRSEMQKLVAETDLVRLVRGKGLL 360

Query: 349 NAIVINDTEDSDTAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTI 408
           NAIVINDTEDS TAW +C+ALK+NGLLAKPTHGNIIRFAPPLV+T+E+L DC  II KTI
Sbjct: 361 NAIVINDTEDSSTAWNICVALKDNGLLAKPTHGNIIRFAPPLVMTKEELLDCISIIRKTI 420

Query: 409 QNFK 412
             FK
Sbjct: 421 LQFK 424


Lambda     K      H
   0.318    0.137    0.407 

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: 613
Number of extensions: 16
Number of successful extensions: 3
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: 413
Length of database: 425
Length adjustment: 32
Effective length of query: 381
Effective length of database: 393
Effective search space:   149733
Effective search space used:   149733
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_054559146.1 I595_RS09190 (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.2164294.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-201  654.3   0.0   3.9e-201  653.9   0.0    1.1  1  NCBI__GCF_001306415.1:WP_054559146.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001306415.1:WP_054559146.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.9   0.0  3.9e-201  3.9e-201       1     401 [.       9     420 ..       9     421 .. 0.96

  Alignments for each domain:
  == domain 1  score: 653.9 bits;  conditional E-value: 3.9e-201
                             TIGR01885   1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlss 73 
                                           s+e+i+le+kyga+nyhplpvvls++eG++vwdvegk+y+dflsaysavnqGhchpki++al++qa++ltl+s
  NCBI__GCF_001306415.1:WP_054559146.1   9 SQEAIDLENKYGAQNYHPLPVVLSRGEGVFVWDVEGKKYYDFLSAYSAVNQGHCHPKIINALKNQAENLTLTS 81 
                                           6899********************************************************************* PP

                             TIGR01885  74 rafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavi 146
                                           rafynd++g+++++ t++fG+dk+lpmntGaeaveta+klarkWgy+kk+ip++ka+i+++++nfhGrt+++i
  NCBI__GCF_001306415.1:WP_054559146.1  82 RAFYNDMLGKYEKFATEFFGFDKLLPMNTGAEAVETALKLARKWGYEKKGIPANKAKIIVCQNNFHGRTISII 154
                                           ************************************************************************* PP

                             TIGR01885 147 slstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckky 219
                                           s+s+dp ++enfGp++p++ +i+yn+++al eal++  e+vaaf+vePiqGeaGv vpd++y+k++ elck +
  NCBI__GCF_001306415.1:WP_054559146.1 155 SASNDPVATENFGPFTPGMLSIRYNDIAALAEALKD--EHVAAFMVEPIQGEAGVYVPDENYIKEAFELCKSK 225
                                           ***********************************9..9********************************** PP

                             TIGR01885 220 nvlliadeiqtGiartGkll.......avehe.....evkPdivllGkalsgGvyPvsavladkevmltikpg 280
                                           nvl+iade+qtGiartG+ll       +++ +     +vkPd+++lGka+sgGv+Pvsavla++++m +i+pg
  NCBI__GCF_001306415.1:WP_054559146.1 226 NVLFIADEVQTGIARTGRLLascgncsCSDKNcsgvpDVKPDVLILGKAISGGVFPVSAVLANNDIMEVIRPG 298
                                           *******************9443333322322556669*********************************** PP

                             TIGR01885 281 ehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkkl..kkeivkevrGkGllnaivideskan 351
                                           +hGst+gGnPla+ava+aalev+kee+lae+a +lGe +r+e++kl  ++++v+ vrGkGllnaivi++++ +
  NCBI__GCF_001306415.1:WP_054559146.1 299 NHGSTFGGNPLACAVAIAALEVVKEENLAENAFQLGELFRSEMQKLvaETDLVRLVRGKGLLNAIVINDTE-D 370
                                           *********************************************977789******************99.9 PP

                             TIGR01885 352 greawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                           + +aw++c+ lk++Gllakpth++iir+aPPlv+t+eel ++++ii+k++
  NCBI__GCF_001306415.1:WP_054559146.1 371 SSTAWNICVALKDNGLLAKPTHGNIIRFAPPLVMTKEELLDCISIIRKTI 420
                                           ***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (425 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: 24.46
//
[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:

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