Alignments for a candidate for glnA in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Desulfallas geothermicus DSM 3669

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_092487048.1 BM299_RS16600 type I glutamate--ammonia ligase

Query= BRENDA::P12425
         (444 letters)



>NCBI__GCF_900115975.1:WP_092487048.1
          Length = 440

 Score =  574 bits (1479), Expect = e-168
 Identities = 279/439 (63%), Positives = 340/439 (77%), Gaps = 1/439 (0%)

Query: 6   REDIEKLVKEENVKYIRLQFTDILGTIKNVEIPVSQLGKALDNKVMFDGSSIEGFVRIEE 65
           + D+    +EE VK+IRLQFTD+LG +KNV I V QL KALD ++MFDGSSI GF RIEE
Sbjct: 3   KRDVIARAREEGVKFIRLQFTDLLGVMKNVAITVDQLEKALDGELMFDGSSIYGFTRIEE 62

Query: 66  SDMYLYPDLNTFVIFPWTAEKGKVARFICDIYNPDGTPFEGDPRNNLKRILKEMEDLGFS 125
           SDMYL PD +TFV+FPW    G VAR +CDIYNPDGTPFEG PR  LKR L +  +LG++
Sbjct: 63  SDMYLRPDPDTFVVFPWRPRDGGVARLMCDIYNPDGTPFEGCPRLTLKRALAKAAELGYT 122

Query: 126 DFNLGPEPEFFLFKLDEKGEPTLELNDKGGYFDLAPTDLGENCRRDIVLELEEMGFEIEA 185
             ++GPE EFFLF LDE  +PTL+ +D+ GYFDL+P DLGE  RRDIVL LEEMGFEIEA
Sbjct: 123 -MHVGPELEFFLFCLDEDEKPTLKTHDQAGYFDLSPVDLGEQARRDIVLTLEEMGFEIEA 181

Query: 186 SHHEVAPGQHEIDFKYAGAVRSCDDIQTFKLVVKTIARKHGLHATFMPKPLFGVNGSGMH 245
           SHHEVAPGQHEIDFKY+ A+ + D I TFK VV+TIA++HGLHATFMPKP+FG+NGSGMH
Sbjct: 182 SHHEVAPGQHEIDFKYSDALDTADKIMTFKFVVRTIAQQHGLHATFMPKPVFGINGSGMH 241

Query: 246 CNLSLFKNGVNAFFDENADLQLSETAKHFIAGIVKHATSFTAVTNPTVNSYKRLVPGYEA 305
            N SLFK   NAF+DEN  +QLS+ A ++I G++KHA +  A+TNPTVNSYKRLVPGYEA
Sbjct: 242 TNQSLFKGNSNAFYDENGPMQLSKEAYYYIGGLLKHARALAAITNPTVNSYKRLVPGYEA 301

Query: 306 PCYVAWSAQNRSPLIRIPASRGISTRVEVRSVDPAANPYLALSVLLAAGLDGIKNKLEAP 365
           P Y+AWS +NRSPLIRIPA RG STRVE+R+ DP+ NPYLAL+  L AGLDGI N++E P
Sbjct: 302 PVYLAWSGRNRSPLIRIPAKRGQSTRVELRNPDPSCNPYLALAACLTAGLDGINNQIEPP 361

Query: 366 APIDRNIYVMSKEERMENGIVDLPATLAEALEEFKSNEVMVKALGEHLFEHFIEAKEIEW 425
              DRNIY M+  E  E GI  LPA+L EA  E   +EV+  ALG+H++E   EAK+ EW
Sbjct: 362 PACDRNIYQMTDAELKELGIGSLPASLQEAFAELAKDEVVRGALGDHIYEKLTEAKQTEW 421

Query: 426 DMFRTQVHPWEREQYMSQY 444
           + FR QVH WE ++Y++ +
Sbjct: 422 NSFRMQVHQWEIDRYLTMF 440


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: 627
Number of extensions: 20
Number of successful extensions: 2
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: 440
Length adjustment: 32
Effective length of query: 412
Effective length of database: 408
Effective search space:   168096
Effective search space used:   168096
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_092487048.1 BM299_RS16600 (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.29472.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-184  598.3   0.0   4.9e-182  591.7   0.0    2.0  1  lcl|NCBI__GCF_900115975.1:WP_092487048.1  BM299_RS16600 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092487048.1  BM299_RS16600 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.7   0.0  4.9e-182  4.9e-182       3     461 ..       6     437 ..       4     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 591.7 bits;  conditional E-value: 4.9e-182
                                 TIGR00653   3 vlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpet 71 
                                               v++ ++ee vkf++l+f+D+ G++k+v+i v++le +al+  ++FDgss++Gf++ieesD++l pdp+t
  lcl|NCBI__GCF_900115975.1:WP_092487048.1   6 VIARAREEGVKFIRLQFTDLLGVMKNVAITVDQLE-KALDGELMFDGSSIYGFTRIEESDMYLRPDPDT 73 
                                               778899****************************6.9******************************** PP

                                 TIGR00653  72 lvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvefk 138
                                               +v++P+r  +  v+r++cd+y+p +++p+e++pR ++kra+ +  ++lg+++ +GpE EFflf  +e +
  lcl|NCBI__GCF_900115975.1:WP_092487048.1  74 FVVFPWRPRDggVARLMCDIYNP-DGTPFEGCPRLTLKRALAKA-AELGYTMHVGPELEFFLFCLDEDE 140
                                               *******99899***********.******************99.5*****************998888 PP

                                 TIGR00653 139 easnssflevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHE 207
                                               +                         ++k++++ gYfd+ pvD  ++ rr++vl+lee+g+e+e+sHHE
  lcl|NCBI__GCF_900115975.1:WP_092487048.1 141 KP------------------------TLKTHDQAGYFDLSPVDLGEQARRDIVLTLEEMGFEIEASHHE 185
                                               54........................7999*************************************** PP

                                 TIGR00653 208 vataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlf 276
                                               va++q+Eid+k+++++++aD+i+++K+vv+++a++hG++atFmpKp+fg ngsGmH+++sl+k + n+f
  lcl|NCBI__GCF_900115975.1:WP_092487048.1 186 VAPGQHEIDFKYSDALDTADKIMTFKFVVRTIAQQHGLHATFMPKPVFGINGSGMHTNQSLFKGNSNAF 254
                                               ********************************************************************* PP

                                 TIGR00653 277 ageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasan 345
                                               ++e+g ++Ls++a yyigG+lkHa+alaA+tnptvnsYkRLvpGyEAPvyla+s +nRs+liRiPa + 
  lcl|NCBI__GCF_900115975.1:WP_092487048.1 255 YDENGPMQLSKEAYYYIGGLLKHARALAAITNPTVNSYKRLVPGYEAPVYLAWSGRNRSPLIRIPAKR- 322
                                               *****888************************************************************. PP

                                 TIGR00653 346 pkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeea 414
                                               ++++R+E+R pDps+npYLa+aa l+AgldGi+n+i+p+ ++d+n+y+++ +elkelGi +lp+sL+ea
  lcl|NCBI__GCF_900115975.1:WP_092487048.1 323 GQSTRVELRNPDPSCNPYLALAACLTAGLDGINNQIEPPPACDRNIYQMTDAELKELGIGSLPASLQEA 391
                                               ********************************************************************* PP

                                 TIGR00653 415 ldelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyl 461
                                               + el++d ev++++lg++++e+  e+k++E++++r++vh++E+ +yl
  lcl|NCBI__GCF_900115975.1:WP_092487048.1 392 FAELAKD-EVVRGALGDHIYEKLTEAKQTEWNSFRMQVHQWEIDRYL 437
                                               *******.*************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (440 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.15
//
[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