GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Azorhizobium caulinodans ORS 571

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012168732.1 AZC_RS01015 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000010525.1:WP_012168732.1
          Length = 382

 Score =  293 bits (751), Expect = 4e-84
 Identities = 157/382 (41%), Positives = 225/382 (58%), Gaps = 8/382 (2%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           M   ++L +L+ F +V   PN +++++++ +L  HGIA +++  P+G ++N+FATIGP +
Sbjct: 1   MSTLDLLDRLIAFPTVSRDPNRELIAFVQAFLGQHGIASEIIATPDGRKANLFATIGPTD 60

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
             G ++SGH DVVP     WT+DPFRLRV   R YGRG  DMKGFLAA LA   + AA P
Sbjct: 61  RPGIMLSGHTDVVPVEGQAWTADPFRLRVADGRAYGRGAADMKGFLAAALALAARAAARP 120

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180
           L  PLHLALS+DEE GC GV  +I RL     +P   IIGEPT +R    HKGK AAR T
Sbjct: 121 LETPLHLALSHDEEVGCVGVRSLIERLSTASVRPRLCIIGEPTSLRVATGHKGKLAARAT 180

Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV-GGPFEHVFEPPYSSLQIGTVKGG 239
             G  GHS+   + LNAIH     +       DR+   G  +  ++ PY++L  G + GG
Sbjct: 181 CCGVEGHSALAPKALNAIHLACDFVGLLRTHQDRIAESGARDADYDIPYTTLHAGVIAGG 240

Query: 240 QAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTT------LGFEVEWQELSAYP 293
            A+NI+P+ C V+FE R I+  D +E+L  +   A  L           ++  + ++ YP
Sbjct: 241 TALNIVPNRCTVDFEIRNIAQDDASEVLTRLLDDAARLVAERRAAFPAADIAVEVVNDYP 300

Query: 294 ALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQ-RAGIDAIICGPGDIGRAHKPDEY 352
            L+   +A + A ++ L    +   V++GTE GLF  R  I  +ICGPG + + HKPDE+
Sbjct: 301 GLATPKEAEVVAFVQALVDDASTFKVAFGTEGGLFDARLSIPTVICGPGSMDQGHKPDEF 360

Query: 353 ILIDELMACRAMVEALGARCTA 374
           I +D+L AC  M++ L  R  A
Sbjct: 361 IALDQLEACDRMMDRLLHRLAA 382


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: 356
Number of extensions: 19
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: 382
Length adjustment: 30
Effective length of query: 344
Effective length of database: 352
Effective search space:   121088
Effective search space used:   121088
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 WP_012168732.1 AZC_RS01015 (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.2602911.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-116  373.4   0.2     7e-116  373.2   0.2    1.0  1  NCBI__GCF_000010525.1:WP_012168732.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012168732.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.2   0.2    7e-116    7e-116       2     364 ..       6     376 ..       5     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 373.2 bits;  conditional E-value: 7e-116
                             TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvd 74 
                                           +l +L+af++vs+ +n +li +v+++l ++g+a e + ++dg  k nl+a+iGp++ + g++lsGhtDvvPv+
  NCBI__GCF_000010525.1:WP_012168732.1   6 LLDRLIAFPTVSRDPNRELIAFVQAFLGQHGIASEIIATPDG-RKANLFATIGPTD-RPGIMLSGHTDVVPVE 76 
                                           6899**************************************.9***********9.**************** PP

                             TIGR01892  75 eaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala. 146
                                           ++aWt+DpfrL++ dgr YgrG+aDmkGFla++La +   aa +L  Plhl+ls Deevg+ G+++lie+l  
  NCBI__GCF_000010525.1:WP_012168732.1  77 GQAWTADPFRLRVADGRAYGRGAADMKGFLAAALALAARAAARPLETPLHLALSHDEEVGCVGVRSLIERLSt 149
                                           *************************************9*******************************9988 PP

                             TIGR01892 147 ..rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edle 216
                                              rp+l i+GePtsl+    hkGk +a+ t  G eghs+ + + ++ai+la ++++ l + +d++ + +  +
  NCBI__GCF_000010525.1:WP_012168732.1 150 asVRPRLCIIGEPTSLRVATGHKGKLAARATCCGVEGHSALAPKALNAIHLACDFVGLLRTHQDRIAEsGARD 222
                                           889***************************************************************9978889 PP

                             TIGR01892 217 eaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.vkek...apgfevkvee 285
                                             ++ py+tl+ G++ GG+a ni+++ C + +e+R i+  d +e+l+ l + a+  v e+    p+ ++ ve+
  NCBI__GCF_000010525.1:WP_012168732.1 223 ADYDIPYTTLHAGVIAGGTALNIVPNRCTVDFEIRNIAQDDASEVLTRLLDDAARlVAERraaFPAADIAVEV 295
                                           99***************************************99988776655555244331115888999*** PP

                             TIGR01892 286 lsatpaleleedaelvalleklaGa.aaevvsygteagllq.elGieavvlGPGdidqahqpdeYveieelkr 356
                                           ++ +p+l+++++ae+va+++ l  + ++  v++gte gl+  +l i++v++GPG++dq h+pde++ +++l++
  NCBI__GCF_000010525.1:WP_012168732.1 296 VNDYPGLATPKEAEVVAFVQALVDDaSTFKVAFGTEGGLFDaRLSIPTVICGPGSMDQGHKPDEFIALDQLEA 368
                                           ***********************9977889**********6479***************************** PP

                             TIGR01892 357 crallerl 364
                                           c+ ++ rl
  NCBI__GCF_000010525.1:WP_012168732.1 369 CDRMMDRL 376
                                           *****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (382 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.29
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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