Alignments for a candidate for glnA in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Thermomonospora curvata DSM 43183

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_012853432.1 TCUR_RS15300 type I glutamate--ammonia ligase

Query= BRENDA::P64246
         (446 letters)



>NCBI__GCF_000024385.1:WP_012853432.1
          Length = 453

 Score =  620 bits (1600), Expect = 0.0
 Identities = 309/454 (68%), Positives = 361/454 (79%), Gaps = 10/454 (2%)

Query: 1   MDRQKEFVLRTLEERDIRFVRLWFTDVLGFLKSVAIAPAELEGAFEEGIGFDGSSIEGFA 60
           MDRQ+EFVLRTLEERDIRF+RLWFTDVLGFLKSVA+APAELEGAF EGIGFDGS+IEGFA
Sbjct: 1   MDRQQEFVLRTLEERDIRFIRLWFTDVLGFLKSVAVAPAELEGAFAEGIGFDGSAIEGFA 60

Query: 61  RVSESDTVAHPDPSTFQVLPWATSSGHHHSARMFCDITMPDGSPSWADPRHVLRRQLTKA 120
           RV E+D +A PDP+TFQ+LPW + +    +ARMFCDI MPDG+PS+ADPR+VL+R L KA
Sbjct: 61  RVFEADMIAKPDPATFQILPWRSEAPG--TARMFCDILMPDGTPSFADPRYVLKRALAKA 118

Query: 121 GELGFSCYVHPEIEFFLLKPGPEDGSVPVPVDNAGYFDQAVHDSALNFRRHAIDALEFMG 180
            +LGF+ Y HPEIEFFL K  PEDGS P PVD  GYFD   H +A +FRR+AI  LE MG
Sbjct: 119 ADLGFTFYTHPEIEFFLFKNLPEDGSEPDPVDAGGYFDHTPHSTAHDFRRNAIMMLEAMG 178

Query: 181 ISVEFSHHEGAPGQQEIDLRFADALSMADNVMTFRYVIKEVALEEGARASFMPKPFGQHP 240
           ISVE+SHHEGAPGQQEIDLR+ADAL+ ADN+MTFR V+KEVALE+G  ASFMPKPF  HP
Sbjct: 179 ISVEYSHHEGAPGQQEIDLRYADALTTADNIMTFRLVMKEVALEQGVWASFMPKPFTDHP 238

Query: 241 GSAMHTHMSLFEGDVNAFHSADDPLQLSEVGKSFIAGILEHACEISAVTNQWVNSYKRL- 299
           GS MHTHMSLFEGD NAF+      QLS+V ++FIAG+L HA EI+AVTNQ+VNSYKRL 
Sbjct: 239 GSGMHTHMSLFEGDRNAFYEPGAEYQLSKVARAFIAGLLRHAAEITAVTNQFVNSYKRLW 298

Query: 300 -------VQGGEAPTAASWGAANRSALVRVPMYTPHKTSSRRVEVRSPDSACNPYLTFAV 352
                    GGEAP+   WG  NRSALVRVPMY PHK  S R+E RS D+A NPYL FA 
Sbjct: 299 GGVGASAGAGGEAPSYICWGHNNRSALVRVPMYKPHKGHSTRIEFRSLDTAANPYLAFAA 358

Query: 353 LLAAGLRGVEKGYVLGPQAEDNVWDLTPEERRAMGYRELPSSLDSALRAMEASELVAEAL 412
           +L AGL+G+E+GY L P AED+VW L+P ERRA+G   LP SLD A++AME SEL+AE L
Sbjct: 359 ILGAGLKGIEEGYELPPGAEDDVWALSPAERRALGIEPLPQSLDEAIKAMERSELMAEVL 418

Query: 413 GEHVFDFFLRNKRTEWANYRSHVTPYELRTYLSL 446
           GEHVFDFFLRNKR EW  YR  VT +E + ++++
Sbjct: 419 GEHVFDFFLRNKRAEWEEYRRQVTDWERKRHIAV 452


Lambda     K      H
   0.320    0.134    0.408 

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: 745
Number of extensions: 22
Number of successful extensions: 3
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: 446
Length of database: 453
Length adjustment: 33
Effective length of query: 413
Effective length of database: 420
Effective search space:   173460
Effective search space used:   173460
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_012853432.1 TCUR_RS15300 (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.10544.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-142  459.3   0.0   1.1e-139  452.0   0.0    2.0  1  lcl|NCBI__GCF_000024385.1:WP_012853432.1  TCUR_RS15300 type I glutamate--a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012853432.1  TCUR_RS15300 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.0   0.0  1.1e-139  1.1e-139       3     460 ..       8     449 ..       6     451 .. 0.95

  Alignments for each domain:
  == domain 1  score: 452.0 bits;  conditional E-value: 1.1e-139
                                 TIGR00653   3 vlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpet 71 
                                               vl++l+e++++f++l f+D+ G+lk+v++   ele  a+ egi FDgs++eGf ++ e+D++ kpdp t
  lcl|NCBI__GCF_000024385.1:WP_012853432.1   8 VLRTLEERDIRFIRLWFTDVLGFLKSVAVAPAELE-GAFAEGIGFDGSAIEGFARVFEADMIAKPDPAT 75 
                                               5678899***************************6.9******************************** PP

                                 TIGR00653  72 lvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvefk 138
                                               ++i+P+r+e   ++r++cd+  p +++p+ +dpR+++kra+ +  ++lg ++y  pE+EFflf++   +
  lcl|NCBI__GCF_000024385.1:WP_012853432.1  76 FQILPWRSEApgTARMFCDILMP-DGTPSFADPRYVLKRALAKA-ADLGFTFYTHPEIEFFLFKNLPED 142
                                               ********9999***********.*******************9.5******************99887 PP

                                 TIGR00653 139 easnssflevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHE 207
                                                +                        +  + + ggYfd +p  +a+d+rr+ +++le++g++ve+sHHE
  lcl|NCBI__GCF_000024385.1:WP_012853432.1 143 GS------------------------EPDPVDAGGYFDHTPHSTAHDFRRNAIMMLEAMGISVEYSHHE 187
                                               33........................567999************************************* PP

                                 TIGR00653 208 vataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlf 276
                                                a++q+Eid+++++++++aD+i+++++v+k va ++G  a+FmpKp++ ++gsGmH+h+sl++  +n+f
  lcl|NCBI__GCF_000024385.1:WP_012853432.1 188 GAPGQQEIDLRYADALTTADNIMTFRLVMKEVALEQGVWASFMPKPFTDHPGSGMHTHMSLFEGDRNAF 256
                                               ********************************************************************* PP

                                 TIGR00653 277 ageegyagLsetalyyigGilkHakalaAltnptvnsYkRLv........pGyEAPvylaysaknRsal 337
                                               +++ +  +Ls+ a+ +i+G+l+Ha  ++A+tn  vnsYkRL         +G EAP y++++++nRsal
  lcl|NCBI__GCF_000024385.1:WP_012853432.1 257 YEPGAEYQLSKVARAFIAGLLRHAAEITAVTNQFVNSYKRLWggvgasagAGGEAPSYICWGHNNRSAL 325
                                               ****9555*********************************722233333467**************** PP

                                 TIGR00653 338 iRiPasa..npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGi 404
                                               +R+P+++  +++++RiE+Rs D++anpYLafaa+l Agl Gi++  + +   + +++ ls++e++ lGi
  lcl|NCBI__GCF_000024385.1:WP_012853432.1 326 VRVPMYKphKGHSTRIEFRSLDTAANPYLAFAAILGAGLKGIEEGYELPPGAEDDVWALSPAERRALGI 394
                                               ******988999********************************************************* PP

                                 TIGR00653 405 eqlpesLeealdelesdkevlkevlgeelieafielkrkEveelrlkvhpvEleky 460
                                               e lp+sL+ea++++e+  e++ evlge++++ f+  kr+E+ee+r +v+++E ++ 
  lcl|NCBI__GCF_000024385.1:WP_012853432.1 395 EPLPQSLDEAIKAMERS-ELMAEVLGEHVFDFFLRNKRAEWEEYRRQVTDWERKRH 449
                                               *****************.**********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (453 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 2.61
//
[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