Alignments for a candidate for rocD in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocD in Beijerinckia indica ATCC 9039

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_012385734.1 BIND_RS14190 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000019845.1:WP_012385734.1
          Length = 412

 Score =  416 bits (1070), Expect = e-121
 Identities = 204/395 (51%), Positives = 274/395 (69%), Gaps = 3/395 (0%)

Query: 9   EIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQAL 68
           + IDQ   +GA+NY PLP+V+S   GA++ D +G  Y+DM+SAYSA + GH HP+++ AL
Sbjct: 4   DFIDQEERFGAHNYAPLPVVLSHGQGAFLFDCDGRRYLDMMSAYSAASFGHLHPRLVGAL 63

Query: 69  KDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVK 128
           K Q +++ L SRA+H D LGPF E  A+LTG +  LPMNTGAEAVE+A+KAARR+ Y+  
Sbjct: 64  KRQLERLDLVSRAYHTDTLGPFCEDLARLTGLDACLPMNTGAEAVETAIKAARRYGYDRL 123

Query: 129 GVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITP 188
            + ++QAEII   GNFHGRT   +  SS+   +RGFGP  PG  L+P+GD  AL  A+ P
Sbjct: 124 SIPEDQAEIIVAAGNFHGRTTTIIGFSSDAATRRGFGPFAPGFVLVPFGDAGALEAAVGP 183

Query: 189 NTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDG 248
            TAA L EPIQGEAGI++PP G+L     +C    +L I DE+Q+G GRTG+TFA + +G
Sbjct: 184 RTAAVLIEPIQGEAGIILPPPGYLAALRRLCDRHGILLIFDEVQSGFGRTGRTFAFEHEG 243

Query: 249 IVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLED 308
             PD  ILGKALGGG+ P+S  AA R ++ VF+PGSHGSTFGGNPLA AV+  ++ VL++
Sbjct: 244 AKPDGLILGKALGGGLLPVSAFAAKRSLMDVFDPGSHGSTFGGNPLAMAVAREAMHVLQE 303

Query: 309 EKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEA---ARPYCERLKEEGLL 365
           E L +RS +LG      L +ID P +  VRG+GL+ GV+L  A   A+  C ++ E G+L
Sbjct: 304 EHLVERSEKLGGVLLDALRAIDHPAVLAVRGKGLWAGVDLDPALADAKKVCLKMMERGVL 363

Query: 366 CKETHDTVIRFAPPLIISKEDLDWAIEKIKHVLRN 400
            KETH T IRFAPPL+I++ DL  A+   + VL +
Sbjct: 364 TKETHATTIRFAPPLVITEADLLEAVGIFRAVLES 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: 473
Number of extensions: 14
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: 412
Length adjustment: 31
Effective length of query: 370
Effective length of database: 381
Effective search space:   140970
Effective search space used:   140970
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_012385734.1 BIND_RS14190 (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.30360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-151  488.5   0.0   7.7e-151  488.3   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012385734.1  BIND_RS14190 ornithine--oxo-acid


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012385734.1  BIND_RS14190 ornithine--oxo-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.3   0.0  7.7e-151  7.7e-151       3     401 ..       4     396 ..       2     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 488.3 bits;  conditional E-value: 7.7e-151
                                 TIGR01885   3 evieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltl 71 
                                               + i++ee++gahny plpvvls+++Ga+++d +g+ryld++saysa + Gh hp++v al+ q ++l l
  lcl|NCBI__GCF_000019845.1:WP_012385734.1   4 DFIDQEERFGAHNYAPLPVVLSHGQGAFLFDCDGRRYLDMMSAYSAASFGHLHPRLVGALKRQLERLDL 72 
                                               6799***************************************************************** PP

                                 TIGR01885  72 ssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhG 140
                                                sra+++d++g f e +++l G d +lpmntGaeavetaik ar++gy++  iped+a i++a+gnfhG
  lcl|NCBI__GCF_000019845.1:WP_012385734.1  73 VSRAYHTDTLGPFCEDLARLTGLDACLPMNTGAEAVETAIKAARRYGYDRLSIPEDQAEIIVAAGNFHG 141
                                               ********************************************************************* PP

                                 TIGR01885 141 rtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgyl 209
                                               rt ++i  s+d  +r++fGp++p++  ++++++ ale a+   g++ aa+l+ePiqGeaG+++p  gyl
  lcl|NCBI__GCF_000019845.1:WP_012385734.1 142 RTTTIIGFSSDAATRRGFGPFAPGFVLVPFGDAGALEAAV---GPRTAAVLIEPIQGEAGIILPPPGYL 207
                                               *************************************986...569*********************** PP

                                 TIGR01885 210 kkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltik 278
                                                  r lc+++ +lli de+q G +rtG+ +a+ehe+ kPd ++lGkal+gG++Pvsa  a++++m +++
  lcl|NCBI__GCF_000019845.1:WP_012385734.1 208 AALRRLCDRHGILLIFDEVQSGFGRTGRTFAFEHEGAKPDGLILGKALGGGLLPVSAFAAKRSLMDVFD 276
                                               ********************************************************************* PP

                                 TIGR01885 279 pgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivide 347
                                               pg+hGst+gGnPla ava +a++vl+ee+l+er+eklG +l ++l+++ ++ v  vrGkGl +++ +d+
  lcl|NCBI__GCF_000019845.1:WP_012385734.1 277 PGSHGSTFGGNPLAMAVAREAMHVLQEEHLVERSEKLGGVLLDALRAIDHPAVLAVRGKGLWAGVDLDP 345
                                               ********************************************************************* PP

                                 TIGR01885 348 skangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                                    ++a ++clk++e+G+l+k+th + ir+aPPlvite +l eav i++ vl
  lcl|NCBI__GCF_000019845.1:WP_012385734.1 346 AL---ADAKKVCLKMMERGVLTKETHATTIRFAPPLVITEADLLEAVGIFRAVL 396
                                               *9...78899***************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (412 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.97
//
[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 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