GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Lentibacillus jeotgali Grbi

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_029329000.1 ON01_RS05550 type I glutamate--ammonia ligase

Query= BRENDA::P12425
         (444 letters)



>NCBI__GCF_000224785.1:WP_029329000.1
          Length = 445

 Score =  731 bits (1886), Expect = 0.0
 Identities = 344/439 (78%), Positives = 393/439 (89%)

Query: 6   REDIEKLVKEENVKYIRLQFTDILGTIKNVEIPVSQLGKALDNKVMFDGSSIEGFVRIEE 65
           ++DI K++ EE+V++IRLQFTD+LGTIKNVEIP SQL KA DNK+MFDGSSIEGFVRI+E
Sbjct: 7   KQDIYKMIDEESVRFIRLQFTDMLGTIKNVEIPYSQLEKAFDNKMMFDGSSIEGFVRIDE 66

Query: 66  SDMYLYPDLNTFVIFPWTAEKGKVARFICDIYNPDGTPFEGDPRNNLKRILKEMEDLGFS 125
           SDMYLYPDL+TFV+FPWTAEKGKVARFICDIYNPDGTPFEG PR NLKR LK ME+LG+S
Sbjct: 67  SDMYLYPDLDTFVVFPWTAEKGKVARFICDIYNPDGTPFEGCPRYNLKRNLKRMEELGYS 126

Query: 126 DFNLGPEPEFFLFKLDEKGEPTLELNDKGGYFDLAPTDLGENCRRDIVLELEEMGFEIEA 185
            FN+G EPEFFLFKLDEKG+P +ELND+GGYFDLAPTDLGENCRRDIVLELEEMGFEIEA
Sbjct: 127 AFNIGTEPEFFLFKLDEKGDPMMELNDRGGYFDLAPTDLGENCRRDIVLELEEMGFEIEA 186

Query: 186 SHHEVAPGQHEIDFKYAGAVRSCDDIQTFKLVVKTIARKHGLHATFMPKPLFGVNGSGMH 245
           SHHEVAPGQHEIDFKY+ AV+  DDIQTFKLVVKTIARKH LHATFMPKPLFGVNGSGMH
Sbjct: 187 SHHEVAPGQHEIDFKYSDAVKHADDIQTFKLVVKTIARKHNLHATFMPKPLFGVNGSGMH 246

Query: 246 CNLSLFKNGVNAFFDENADLQLSETAKHFIAGIVKHATSFTAVTNPTVNSYKRLVPGYEA 305
            N+SLFK+G N F+DE  D+Q+S T K F AGI+KHAT+FTAVTNPTVNSYKRLVPGYEA
Sbjct: 247 VNMSLFKDGRNVFYDEKGDMQVSTTLKQFTAGIIKHATNFTAVTNPTVNSYKRLVPGYEA 306

Query: 306 PCYVAWSAQNRSPLIRIPASRGISTRVEVRSVDPAANPYLALSVLLAAGLDGIKNKLEAP 365
           PCYVAWS  NRSPL+R+P+SRG+STR+E RSVDPAANPY+ L+VLL+AGLDGI+NKL  P
Sbjct: 307 PCYVAWSGLNRSPLVRVPSSRGLSTRIEARSVDPAANPYMTLAVLLSAGLDGIENKLTPP 366

Query: 366 APIDRNIYVMSKEERMENGIVDLPATLAEALEEFKSNEVMVKALGEHLFEHFIEAKEIEW 425
            P+D+NIY M K ER E+GI  LPATL +ALEE  ++ V+ +ALG HL+EHF+EAK+IEW
Sbjct: 367 EPVDQNIYEMDKAEREEHGIKSLPATLMDALEELDNDPVITEALGNHLYEHFVEAKQIEW 426

Query: 426 DMFRTQVHPWEREQYMSQY 444
           DMFRT VHPWEREQY++ Y
Sbjct: 427 DMFRTAVHPWEREQYLTSY 445


Lambda     K      H
   0.319    0.137    0.406 

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: 727
Number of extensions: 24
Number of successful extensions: 1
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: 444
Length of database: 445
Length adjustment: 32
Effective length of query: 412
Effective length of database: 413
Effective search space:   170156
Effective search space used:   170156
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: 51 (24.3 bits)

Align candidate WP_029329000.1 ON01_RS05550 (type I glutamate--ammonia ligase)
to HMM TIGR00653 (glnA: glutamine synthetase, type I (EC 6.3.1.2))

# 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/TIGR00653.hmm
# target sequence database:        /tmp/gapView.2750803.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00653  [M=462]
Accession:   TIGR00653
Description: GlnA: glutamine synthetase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-185  601.4   0.2   4.8e-183  595.0   0.2    2.0  1  NCBI__GCF_000224785.1:WP_029329000.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_029329000.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.0   0.2  4.8e-183  4.8e-183       2     461 ..       9     442 ..       8     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: 595.0 bits;  conditional E-value: 4.8e-183
                             TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 
                                           ++ k+++ee v+f++l+f+D+ G++k+veip+s+le +a++++++FDgss+eGf++i+esD++l+pd++t+v+
  NCBI__GCF_000224785.1:WP_029329000.1   9 DIYKMIDEESVRFIRLQFTDMLGTIKNVEIPYSQLE-KAFDNKMMFDGSSIEGFVRIDESDMYLYPDLDTFVV 80 
                                           6889*******************************6.9*********************************** PP

                             TIGR00653  75 vPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvefkeasnssf 145
                                           +P++aek  v+r+icd+y+p +++p+e++pR+++kr ++++++   + +++G+E+EFflf+ +e+++      
  NCBI__GCF_000224785.1:WP_029329000.1  81 FPWTAEKgkVARFICDIYNP-DGTPFEGCPRYNLKRNLKRMEELGYSAFNIGTEPEFFLFKLDEKGDP----- 147
                                           *****9999***********.********************876677789***********9999855..... PP

                             TIGR00653 146 levdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidik 218
                                                               ++++++ggYfd++p+D  +++rr++vl+lee+g+e+e+sHHEva++q+Eid+k
  NCBI__GCF_000224785.1:WP_029329000.1 148 -------------------MMELNDRGGYFDLAPTDLGENCRRDIVLELEEMGFEIEASHHEVAPGQHEIDFK 201
                                           ...................67899************************************************* PP

                             TIGR00653 219 fdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetaly 291
                                           ++++vk+aD+i+++K+vvk++a+kh ++atFmpKplfg ngsGmHv++sl+kdg+n+f++e+g++++s t + 
  NCBI__GCF_000224785.1:WP_029329000.1 202 YSDAVKHADDIQTFKLVVKTIARKHNLHATFMPKPLFGVNGSGMHVNMSLFKDGRNVFYDEKGDMQVSTTLKQ 274
                                           ***************************************************************999******* PP

                             TIGR00653 292 yigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYL 364
                                           + +Gi+kHa+ ++A+tnptvnsYkRLvpGyEAP+y+a+s  nRs+l+R+P s+ + ++RiE Rs+Dp+anpY+
  NCBI__GCF_000224785.1:WP_029329000.1 275 FTAGIIKHATNFTAVTNPTVNSYKRLVPGYEAPCYVAWSGLNRSPLVRVPSSR-GLSTRIEARSVDPAANPYM 346
                                           ****************************************************9.******************* PP

                             TIGR00653 365 afaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdkevlkevlgeelieaf 437
                                           ++a+ll AgldGi+nk++p+ep+d+n+ye++++e++e+Gi++lp++L +al+el++d  v++e+lg++l+e+f
  NCBI__GCF_000224785.1:WP_029329000.1 347 TLAVLLSAGLDGIENKLTPPEPVDQNIYEMDKAEREEHGIKSLPATLMDALEELDND-PVITEALGNHLYEHF 418
                                           *********************************************************.*************** PP

                             TIGR00653 438 ielkrkEveelrlkvhpvElekyl 461
                                           +e+k+ E++++r++vhp+E e+yl
  NCBI__GCF_000224785.1:WP_029329000.1 419 VEAKQIEWDMFRTAVHPWEREQYL 442
                                           ***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (445 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: 16.01
//
[ok]

This GapMind analysis is from Jul 26 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