Alignments for a candidate for argE in Azorhizobium caulinodans ORS 571

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.12289.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  lcl|NCBI__GCF_000010525.1:WP_012168732.1  AZC_RS01015 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010525.1:WP_012168732.1  AZC_RS01015 acetylornithine deacetylase
   #    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 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDv 70 
                                               +l +L+af++vs+ +n +li +v+++l ++g+a e + ++dg  k nl+a+iGp++ + g++lsGhtDv
  lcl|NCBI__GCF_000010525.1:WP_012168732.1   6 LLDRLIAFPTVSRDPNRELIAFVQAFLGQHGIASEIIATPDG-RKANLFATIGPTD-RPGIMLSGHTDV 72 
                                               6899**************************************.9***********9.************ PP

                                 TIGR01892  71 vPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGak 139
                                               vPv+++aWt+DpfrL++ dgr YgrG+aDmkGFla++La +   aa +L  Plhl+ls Deevg+ G++
  lcl|NCBI__GCF_000010525.1:WP_012168732.1  73 VPVEGQAWTADPFRLRVADGRAYGRGAADMKGFLAAALALAARAAARPLETPLHLALSHDEEVGCVGVR 141
                                               *****************************************9*************************** PP

                                 TIGR01892 140 klieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva 205
                                               +lie+l     rp+l i+GePtsl+    hkGk +a+ t  G eghs+ + + ++ai+la ++++ l +
  lcl|NCBI__GCF_000010525.1:WP_012168732.1 142 SLIERLStasVRPRLCIIGEPTSLRVATGHKGKLAARATCCGVEGHSALAPKALNAIHLACDFVGLLRT 210
                                               ****9988889********************************************************** PP

                                 TIGR01892 206 ladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.v 272
                                                +d++ + +  +  ++ py+tl+ G++ GG+a ni+++ C + +e+R i+  d +e+l+ l + a+  v
  lcl|NCBI__GCF_000010525.1:WP_012168732.1 211 HQDRIAEsGARDADYDIPYTTLHAGVIAGGTALNIVPNRCTVDFEIRNIAQDDASEVLTRLLDDAARlV 279
                                               *****997888999***************************************9998877665555524 PP

                                 TIGR01892 273 kek...apgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllq.elGieavvlGP 336
                                                e+    p+ ++ ve+++ +p+l+++++ae+va+++ l  + ++  v++gte gl+  +l i++v++GP
  lcl|NCBI__GCF_000010525.1:WP_012168732.1 280 AERraaFPAADIAVEVVNDYPGLATPKEAEVVAFVQALVDDaSTFKVAFGTEGGLFDaRLSIPTVICGP 348
                                               4331115888999**************************9977889**********6479********* PP

                                 TIGR01892 337 GdidqahqpdeYveieelkrcrallerl 364
                                               G++dq h+pde++ +++l++c+ ++ rl
  lcl|NCBI__GCF_000010525.1:WP_012168732.1 349 GSMDQGHKPDEFIALDQLEACDRMMDRL 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.14
//
[ok]

This GapMind analysis is from Apr 10 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