Alignments for a candidate for rocD in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocD in Azospirillum brasilense Sp245

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase

Query= SwissProt::P38021
         (401 letters)



>FitnessBrowser__azobra:AZOBR_RS19590
          Length = 405

 Score =  452 bits (1164), Expect = e-132
 Identities = 219/398 (55%), Positives = 283/398 (71%), Gaps = 3/398 (0%)

Query: 4   LSKSKEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPK 63
           L  + ++I      GA+NY PL +V++   G +V D EGN Y+D LSAYSAVNQGH HPK
Sbjct: 2   LQHAADLIGTEHRLGAHNYKPLDVVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPK 61

Query: 64  IIQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRW 123
           I++A+  QA K+TLTSRAF NDQL  FYE+ A LTG   ILPMN+GAEAVESA+K  R+W
Sbjct: 62  ILEAMVQQASKLTLTSRAFRNDQLALFYEELAALTGSHKILPMNSGAEAVESAIKTVRKW 121

Query: 124 AYEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALR 183
            YEV+GV +NQAEII C  NFHGRT+  VS S++ + + GFGP  PG + +P+GD  AL 
Sbjct: 122 GYEVRGVPENQAEIIVCSDNFHGRTISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALE 181

Query: 184 QAITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFA 243
            A+TPNT A L EPIQGEAG+VIPP G+L+    +C E NV+ I DEIQTGLGRTGK  A
Sbjct: 182 AALTPNTVAVLLEPIQGEAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLA 241

Query: 244 CDWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASL 303
            + +G+  D+ ++GKAL GG +P+S + ++ E+LGV  PG HGSTFGGNPLACAV+ A++
Sbjct: 242 EEHEGVEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAM 301

Query: 304 EVLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVEL---TEAARPYCERLK 360
            VL +E + D +   G YF  +L +I S VI+E RGRGL + VEL      AR YCE L+
Sbjct: 302 RVLVEEGMIDNAAAQGAYFLEQLGAIRSNVIREARGRGLMLAVELHPEAGGARRYCEALR 361

Query: 361 EEGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398
             G+L K+THD  IR APPL+I++E +DWA+E+   VL
Sbjct: 362 ARGVLAKDTHDHTIRIAPPLVITREQVDWALEQFDAVL 399


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: 451
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: 405
Length adjustment: 31
Effective length of query: 370
Effective length of database: 374
Effective search space:   138380
Effective search space used:   138380
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 AZOBR_RS19590 AZOBR_RS19590 (ornithine-oxoacid aminotransferase)
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.21379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-167  542.5   0.0   3.1e-167  542.3   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS19590  AZOBR_RS19590 ornithine-oxoacid 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS19590  AZOBR_RS19590 ornithine-oxoacid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.3   0.0  3.1e-167  3.1e-167       3     400 ..       7     398 ..       5     400 .. 0.98

  Alignments for each domain:
  == domain 1  score: 542.3 bits;  conditional E-value: 3.1e-167
                                 TIGR01885   3 evieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltl 71 
                                               ++i +e++ gahny+pl+vvl+++eG++vwd+eg+ryld lsaysavnqGhchpki++a+v+qa+kltl
  lcl|FitnessBrowser__azobra:AZOBR_RS19590   7 DLIGTEHRLGAHNYKPLDVVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTL 75 
                                               67899**************************************************************** PP

                                 TIGR01885  72 ssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhG 140
                                               +sraf nd+++ f e ++ l G  k+lpmn+Gaeave+aik +rkWgy+++++pe++a i+++++nfhG
  lcl|FitnessBrowser__azobra:AZOBR_RS19590  76 TSRAFRNDQLALFYEELAALTGSHKILPMNSGAEAVESAIKTVRKWGYEVRGVPENQAEIIVCSDNFHG 144
                                               ********************************************************************* PP

                                 TIGR01885 141 rtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgyl 209
                                               rt++++s stdp++r +fGp++p+++++++++++ale al+    + +a+l+ePiqGeaGvv+p  gyl
  lcl|FitnessBrowser__azobra:AZOBR_RS19590 145 RTISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALEAALTP---NTVAVLLEPIQGEAGVVIPPAGYL 210
                                               ****************************************98...8999******************** PP

                                 TIGR01885 210 kkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltik 278
                                               ++vr+lc++ nv++i deiqtG++rtGklla ehe+v  d+ l+GkalsgG+yPvsavl+++ev+ ++k
  lcl|FitnessBrowser__azobra:AZOBR_RS19590 211 RRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVEADVTLIGKALSGGFYPVSAVLSNSEVLGVLK 279
                                               ********************************************************************* PP

                                 TIGR01885 279 pgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivide 347
                                               pg+hGst+gGnPla+ava aa++vl ee ++++a+  G+ + e+l ++++++++e rG+Gl+ a+ +++
  lcl|FitnessBrowser__azobra:AZOBR_RS19590 280 PGQHGSTFGGNPLACAVARAAMRVLVEEGMIDNAAAQGAYFLEQLGAIRSNVIREARGRGLMLAVELHP 348
                                               ********************************************************************* PP

                                 TIGR01885 348 skangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkv 400
                                               ++     a   c  l+ +G+lak+th++ ir+aPPlvit+e++++a+e +  v
  lcl|FitnessBrowser__azobra:AZOBR_RS19590 349 EA---GGARRYCEALRARGVLAKDTHDHTIRIAPPLVITREQVDWALEQFDAV 398
                                               99...667789***********************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (405 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: 8.95
//
[ok]

This GapMind analysis is from Sep 17 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