GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Dyadobacter tibetensis Y620-1

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_025765140.1 X939_RS0120435 ornithine--oxo-acid transaminase

Query= BRENDA::Q98TS5
         (439 letters)



>NCBI__GCF_000566685.1:WP_025765140.1
          Length = 419

 Score =  519 bits (1337), Expect = e-152
 Identities = 250/405 (61%), Positives = 318/405 (78%), Gaps = 4/405 (0%)

Query: 39  SSEYVFDRESKYGAHNYHPLPVALERGKGVYVWDVEGRRYFDFLSAYSAVNQGHCHPKIL 98
           +S+   D E ++GAHNY P+ V L +G+GV+VWDVEG+ Y DFLSAYSAV+QGHCHPKI+
Sbjct: 12  TSQQAIDLELRFGAHNYKPMSVVLNKGRGVHVWDVEGKEYLDFLSAYSAVSQGHCHPKII 71

Query: 99  DALKSQADKLTLTSRAFYNDVLGEYEEYITKIFGYNKVLPMNTGVEGGETACKLARKWAY 158
            AL +QA KLTLTSRAFYND LG  E+Y+ + FGY+KVL MN+GVE GETA KL RKWAY
Sbjct: 72  QALINQAQKLTLTSRAFYNDQLGPCEQYMAEYFGYDKVLMMNSGVEAGETALKLTRKWAY 131

Query: 159 TVKGIPKYKAQIIFAAGNFWGRTMSAISSSTDPSSYEGFGPFMPGFKIIPYNDLPALERA 218
            VKG+P  +A++++ +GNFWGRT++A+SSSTDPSS   +GPF+PGF+IIPYNDL ALE  
Sbjct: 132 KVKGVPTDQAKMVYVSGNFWGRTLAAVSSSTDPSSTTHYGPFLPGFQIIPYNDLEALESC 191

Query: 219 LQ-DPNVAAFMVEPIQGEAGVIVPDEGYLTGVRQLCTAHNVLFIADEVQTGLARTGKMLA 277
            + DPN+A FMVEPIQGEAGV+VP EGYL GVR LCT + VLFIADEVQTG+ RTGK LA
Sbjct: 192 FKSDPNIAGFMVEPIQGEAGVVVPHEGYLQGVRNLCTQYQVLFIADEVQTGIGRTGKKLA 251

Query: 278 VDHENVRPDLVILGKALSGGVYPVSAVLCDDEVMLTIKPGEHGSTYGGNPLGCRVAMASL 337
            D E V+PD+++LGKALSGGV+PVSA L +DEVMLTI PGEHGST+GGNPL C VA+A+L
Sbjct: 252 CDWEGVKPDILVLGKALSGGVFPVSAALANDEVMLTILPGEHGSTFGGNPLACAVAVAAL 311

Query: 338 EVIEEEKLAENANXMGELLRAEL--MKTPSDIVTAVRGKGLLNAIVIKQSKDCD-AWKVC 394
           +V+EEE LA NA  MG++ R+ +  ++    ++  VRGKGLLNAIVI  S++ D A  +C
Sbjct: 312 KVVEEEDLAANAEAMGQIFRSRMHDLQKQCSLIEIVRGKGLLNAIVINDSEESDTANTLC 371

Query: 395 LRLRDNGLLAKPTHGDIIRLAPPLTIKEDEIRECSEIIHKTLLSF 439
            ++ + GLL KPTHG+ IR APPL I  +++ +  +II +  + F
Sbjct: 372 YQMMEKGLLCKPTHGNKIRFAPPLVINAEQMNQACDIIAEVFIQF 416


Lambda     K      H
   0.318    0.136    0.404 

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: 534
Number of extensions: 12
Number of successful extensions: 4
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: 439
Length of database: 419
Length adjustment: 32
Effective length of query: 407
Effective length of database: 387
Effective search space:   157509
Effective search space used:   157509
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_025765140.1 X939_RS0120435 (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.2128128.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-198  643.9   0.0     5e-198  643.7   0.0    1.0  1  NCBI__GCF_000566685.1:WP_025765140.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000566685.1:WP_025765140.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.7   0.0    5e-198    5e-198       1     400 [.      13     412 ..      13     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 643.7 bits;  conditional E-value: 5e-198
                             TIGR01885   1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlss 73 
                                           s+++i+le ++gahny+p+ vvl+k++G++vwdvegk+yldflsaysav+qGhchpki++al++qaqkltl+s
  NCBI__GCF_000566685.1:WP_025765140.1  13 SQQAIDLELRFGAHNYKPMSVVLNKGRGVHVWDVEGKEYLDFLSAYSAVSQGHCHPKIIQALINQAQKLTLTS 85 
                                           689********************************************************************** PP

                             TIGR01885  74 rafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavi 146
                                           rafynd++g +++y++++fGydkvl+mn+G+ea+eta+kl+rkW+yk+k++p+d+a+++ ++gnf+Grtla++
  NCBI__GCF_000566685.1:WP_025765140.1  86 RAFYNDQLGPCEQYMAEYFGYDKVLMMNSGVEAGETALKLTRKWAYKVKGVPTDQAKMVYVSGNFWGRTLAAV 158
                                           ************************************************************************* PP

                             TIGR01885 147 slstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckky 219
                                           s stdp+s++++Gp++p+++ i+yn+leale+ +++ ++++a+f+vePiqGeaGvvvp++gyl+ vr+lc++y
  NCBI__GCF_000566685.1:WP_025765140.1 159 SSSTDPSSTTHYGPFLPGFQIIPYNDLEALESCFKS-DPNIAGFMVEPIQGEAGVVVPHEGYLQGVRNLCTQY 230
                                           ***********************************9.************************************ PP

                             TIGR01885 220 nvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPla 292
                                           +vl+iade+qtGi+rtGk la+++e+vkPdi++lGkalsgGv+Pvsa la++evmlti pgehGst+gGnPla
  NCBI__GCF_000566685.1:WP_025765140.1 231 QVLFIADEVQTGIGRTGKKLACDWEGVKPDILVLGKALSGGVFPVSAALANDEVMLTILPGEHGSTFGGNPLA 303
                                           ************************************************************************* PP

                             TIGR01885 293 savavaalevlkeeklaeraeklGeelreelkklkk..eivkevrGkGllnaivideskangreawdlclklk 363
                                           +avavaal+v++ee+la +ae +G+++r+++++l+k  ++++ vrGkGllnaivi++s+ ++ +a  lc +++
  NCBI__GCF_000566685.1:WP_025765140.1 304 CAVAVAALKVVEEEDLAANAEAMGQIFRSRMHDLQKqcSLIEIVRGKGLLNAIVINDSE-ESDTANTLCYQMM 375
                                           **********************************774579******************9.999********** PP

                             TIGR01885 364 ekGllakptheeiirlaPPlviteeelkeaveiikkv 400
                                           ekGll kpth++ ir+aPPlvi  e++++a++ii++v
  NCBI__GCF_000566685.1:WP_025765140.1 376 EKGLLCKPTHGNKIRFAPPLVINAEQMNQACDIIAEV 412
                                           **********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (419 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: 20.42
//
[ok]

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

Links

Downloads

Related tools

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