Alignments for a candidate for argE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Paraburkholderia bryophila 376MFSha3.1

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate H281DRAFT_00879 H281DRAFT_00879 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Burk376:H281DRAFT_00879
          Length = 416

 Score =  262 bits (669), Expect = 1e-74
 Identities = 145/364 (39%), Positives = 210/364 (57%), Gaps = 11/364 (3%)

Query: 9   KLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEAR---GYI 65
           +LV   +V   PN  ++  +R  L + GI   +     G  +N+FATI   +     G +
Sbjct: 35  RLVSMDTVSRNPNLGLIETVRDELRALGIEGTLTHDASGKWANLFATIPAHDGETNGGVV 94

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     W SDPF+  +  D+LYGRGT DMKGF+ A LA VP +    L +P+
Sbjct: 95  LSGHTDVVPVDGQQWDSDPFKPEIRGDKLYGRGTCDMKGFIGAALALVPDMQRTKLAKPI 154

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           H ALS+DEE GC G P +IA L +   +P G I+GEPT MR I AHKG  A +  VRG++
Sbjct: 155 HFALSFDEEVGCAGAPLLIADLMKRGVKPDGCIVGEPTSMRPIVAHKGINAYQCCVRGQA 214

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244
            HSS   +GLNAI   A ++      AD+    GPF+ +++ P+++ Q  T+ GG A+N 
Sbjct: 215 AHSSLTPKGLNAIEYAARLICYIRDMADQFREQGPFDELYDVPFTTAQTSTIVGGNAINT 274

Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTA-EALTTLGFE------VEWQELSAYPALSL 297
           +P  C+ +FE R +  +DP  + A + + A E L            +E  +++A P L  
Sbjct: 275 VPAECKFQFEFRNLPTLDPEPIFARIDQYARETLLPKMLREHPLAAIEITKIAAAPGLDS 334

Query: 298 EPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDE 357
              A +  L+  LT  +    V+YGTEAGLF  AGI +I+CGPGDI +AHK +E++ +D+
Sbjct: 335 SEQAAITQLVRALTADQDKRKVAYGTEAGLFSLAGIPSIVCGPGDIQQAHKANEFVALDQ 394

Query: 358 LMAC 361
           L+ C
Sbjct: 395 LVQC 398


Lambda     K      H
   0.319    0.137    0.410 

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: 376
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: 374
Length of database: 416
Length adjustment: 31
Effective length of query: 343
Effective length of database: 385
Effective search space:   132055
Effective search space used:   132055
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: 50 (23.9 bits)

Align candidate H281DRAFT_00879 H281DRAFT_00879 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

# 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.aa/TIGR01892.hmm
# target sequence database:        /tmp/gapView.30697.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01892  [M=365]
Accession:   TIGR01892
Description: AcOrn-deacetyl: acetylornithine deacetylase (ArgE)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.8e-115  370.2   0.0     7e-115  369.9   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00879  H281DRAFT_00879 acetylornithine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00879  H281DRAFT_00879 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.9   0.0    7e-115    7e-115       4     364 ..      34     405 ..      32     406 .. 0.97

  Alignments for each domain:
  == domain 1  score: 369.9 bits;  conditional E-value: 7e-115
                                    TIGR01892   4 akLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpk..egagglvlsGh 67 
                                                  ++Lv++d+vs+ +n+ lie v+d l++lg++      a g +  nl+a+i ++  e +gg+vlsGh
  lcl|FitnessBrowser__Burk376:H281DRAFT_00879  34 TRLVSMDTVSRNPNLGLIETVRDELRALGIEGTLTHDASG-KWANLFATIPAHdgETNGGVVLSGH 98 
                                                  78**********************************9999.99*******988334469******* PP

                                    TIGR01892  68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeev 133
                                                  tDvvPvd+++W sDpf+   + ++LYgrGt+DmkGF+ ++La vpd++ +kL kP+h +ls+Deev
  lcl|FitnessBrowser__Burk376:H281DRAFT_00879  99 TDVVPVDGQQWDSDPFKPEIRGDKLYGRGTCDMKGFIGAALALVPDMQRTKLAKPIHFALSFDEEV 164
                                                  ****************************************************************** PP

                                    TIGR01892 134 glaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaiela 196
                                                  g+aGa+ li+ l+    +p+  ivGePts++++ ahkG+ + +  vrG+ +hss + +G++aie a
  lcl|FitnessBrowser__Burk376:H281DRAFT_00879 165 GCAGAPLLIADLMkrgVKPDGCIVGEPTSMRPIVAHKGINAYQCCVRGQAAHSSLTPKGLNAIEYA 230
                                                  **********99977789************************************************ PP

                                    TIGR01892 197 akllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeel 261
                                                  a+l+  + ++ad+ ++ ++++e +++p++t +  t+ GG+a n ++a+C++++e+R +p +dpe +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00879 231 ARLICYIRDMADQFREqGPFDELYDVPFTTAQTSTIVGGNAINTVPAECKFQFEFRNLPTLDPEPI 296
                                                  **************99799*********************************************** PP

                                    TIGR01892 262 lallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygtea 321
                                                   a + + a e     + +++p   +++ +  a p+l+  e+a + +l++ l+ +   + v+ygtea
  lcl|FitnessBrowser__Burk376:H281DRAFT_00879 297 FARIDQYAREtllpkMLREHPLAAIEITKIAAAPGLDSSEQAAITQLVRALTADqDKRKVAYGTEA 362
                                                  ****9999988888878999*********************************98999******** PP

                                    TIGR01892 322 gllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                  gl+  +Gi+++v+GPGdi+qah+++e+v +++l++c+ +l++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00879 363 GLFSLAGIPSIVCGPGDIQQAHKANEFVALDQLVQCERFLHKF 405
                                                  **************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (416 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.30
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis