Alignments for a candidate for glnA in Thermovibrio ammonificans HB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Thermovibrio ammonificans HB-1

Align glutamine synthetase, type I (characterized)
to candidate WP_013537387.1 THEAM_RS03195 type I glutamate--ammonia ligase

Query= metacyc::SYNPCC7942_2156-MONOMER
         (473 letters)



>NCBI__GCF_000185805.1:WP_013537387.1
          Length = 472

 Score =  570 bits (1469), Expect = e-167
 Identities = 274/471 (58%), Positives = 349/471 (74%), Gaps = 2/471 (0%)

Query: 2   PETAQEVLQLIQEKGIQLVDLKFIDMPGIWQHLTLHVSQIDENSFVEGVPFDGSSIRGWK 61
           P+ A+EV++LIQ +GI+ VDL+F DM G W H+T    +I E SF +G+ FDGSSIR W+
Sbjct: 3   PQNAKEVVELIQREGIKFVDLRFTDMFGTWHHITFPAHEISEESFEQGLFFDGSSIRQWQ 62

Query: 62  AINESDMTMVPDPTTAWIDPFMKEPTLSMICTIYEPRTNTPYERCPRAIAQKAVDYLKAS 121
            IN SDM    DPTTA +DP  + PTL +I  I +P T  PY + PR IA+KA++YLK++
Sbjct: 63  PINASDMMFKLDPTTATVDPLSEIPTLVVIADIVDPVTKEPYHKDPRNIAKKALEYLKST 122

Query: 122 GIGDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREEEGGNLGYKPRYKEG 181
           GIGD  Y GPE EFF+FDDVR+D   N  +Y VDS+EG W +G +E   NLG+K + K G
Sbjct: 123 GIGDAVYCGPEPEFFVFDDVRYDVGMNYGFYEVDSVEGIWRTGADESP-NLGHKVKVKGG 181

Query: 182 YFPVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLMTY 241
           YFPV P D    +R  M L M + G+ +E  HHEVATGGQCE+ FRFG LIEAAD +   
Sbjct: 182 YFPVPPNDQLDHIRKIMALKMEEAGLVVEALHHEVATGGQCEIDFRFGTLIEAADNIQWA 241

Query: 242 KYVIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWNDGQPLFAGDQYAGLSQMALWYI 301
           KY++KNV + +GKT TFMPKPLF DNGSGMHTH SIW +G+ LF GD YAGLS+ AL++I
Sbjct: 242 KYIVKNVAKMFGKTATFMPKPLFGDNGSGMHTHMSIWKNGENLFHGDSYAGLSETALYFI 301

Query: 302 GGILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNPKAKRLE 361
           GGI+KHA A+ A TNPT NSYKRLVPG+EAPVNL YS  NRSA++R+P+  T+ KAKR+E
Sbjct: 302 GGIIKHAKAVCAFTNPTVNSYKRLVPGYEAPVNLCYSARNRSAAIRVPVV-TSSKAKRIE 360

Query: 362 FRCPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTPGSLKDA 421
            R PD++  PYLAF A+L AG+DGI+N+I PGEP+D ++YDL PEEL  IP+ PGSL +A
Sbjct: 361 VRFPDSSGAPYLAFTALLMAGLDGIENKIHPGEPVDKNLYDLPPEELTDIPTVPGSLAEA 420

Query: 422 LKALEADHDFLTVGGVFTEDFIQNWIEYKLDNEVIPISLRPHPYEFALYYD 472
           + ALE D++FLT GGV TE F++++IEYK   E+ P+ LRP P EF LY+D
Sbjct: 421 IDALEKDYEFLTKGGVMTEQFLEDYIEYKRKEEIDPVRLRPTPMEFMLYFD 471


Lambda     K      H
   0.319    0.138    0.428 

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: 711
Number of extensions: 29
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: 473
Length of database: 472
Length adjustment: 33
Effective length of query: 440
Effective length of database: 439
Effective search space:   193160
Effective search space used:   193160
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_013537387.1 THEAM_RS03195 (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.27899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-206  671.7   0.0     3e-206  671.5   0.0    1.0  1  lcl|NCBI__GCF_000185805.1:WP_013537387.1  THEAM_RS03195 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013537387.1  THEAM_RS03195 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.5   0.0    3e-206    3e-206       2     462 .]       8     471 ..       7     471 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.5 bits;  conditional E-value: 3e-206
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               ev++l++ e +kfvdlrf+D+ G+++++++p++e++ee +e+g+ FDgss++ ++ i+ sD+++k dp 
  lcl|NCBI__GCF_000185805.1:WP_013537387.1   8 EVVELIQREGIKFVDLRFTDMFGTWHHITFPAHEISEESFEQGLFFDGSSIRQWQPINASDMMFKLDPT 76 
                                               78999**************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t++++P ++ ++l+vi+d+ +pvtkepy++dpR+iak+a+e+lk t++gd vy GpE+EFf+fd+v+ +
  lcl|NCBI__GCF_000185805.1:WP_013537387.1  77 TATVDPLSEIPTLVVIADIVDPVTKEPYHKDPRNIAKKALEYLKsTGIGDAVYCGPEPEFFVFDDVRYD 145
                                               ********************************************************************* PP

                                 TIGR00653 139 easnssflevdseegewnreveeg.nkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHH 206
                                                 +n+ f+evds+eg w +  +e+ n g+k+k kggYf+v+p+D++  ir+ ++l++ee gl ve+ HH
  lcl|NCBI__GCF_000185805.1:WP_013537387.1 146 VGMNYGFYEVDSVEGIWRTGADESpNLGHKVKVKGGYFPVPPNDQLDHIRKIMALKMEEAGLVVEALHH 214
                                               ******************6666666******************************************** PP

                                 TIGR00653 207 Evata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               Evat+ q Eid++f +l++aaD+i+  Ky+vknvak+ GktatFmpKplfgdngsGmH+h+s+wk+gen
  lcl|NCBI__GCF_000185805.1:WP_013537387.1 215 EVATGgQCEIDFRFGTLIEAADNIQWAKYIVKNVAKMFGKTATFMPKPLFGDNGSGMHTHMSIWKNGEN 283
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                               lf+g++ yagLsetaly+igGi+kHaka+ A+tnptvnsYkRLvpGyEAPv+l+ysa+nRsa+iR+P++
  lcl|NCBI__GCF_000185805.1:WP_013537387.1 284 LFHGDS-YAGLSETALYFIGGIIKHAKAVCAFTNPTVNSYKRLVPGYEAPVNLCYSARNRSAAIRVPVV 351
                                               ******.************************************************************** PP

                                 TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412
                                               ++ kakRiEvR+pD+s+ pYLaf+allmAgldGi+nki+pgep+dknly+l++eel +  i+++p sL+
  lcl|NCBI__GCF_000185805.1:WP_013537387.1 352 TSSKAKRIEVRFPDSSGAPYLAFTALLMAGLDGIENKIHPGEPVDKNLYDLPPEELTD--IPTVPGSLA 418
                                               **********************************************************..********* PP

                                 TIGR00653 413 ealdelesdk..evlkevlgeelieafielkr.kEveelrlkvhpvElekyld 462
                                               ea+d+le+d+  +++++v++e+++e +ie+kr +E++++rl+++p+E++ y+d
  lcl|NCBI__GCF_000185805.1:WP_013537387.1 419 EAIDALEKDYefLTKGGVMTEQFLEDYIEYKRkEEIDPVRLRPTPMEFMLYFD 471
                                               **********888999****************889****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (472 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.40
//
[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