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.738064.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.16
//
[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:

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