Alignments for a candidate for glnA in Oleispira antarctica RB-8

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Oleispira antarctica RB-8

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_046007614.1 OLEAN_RS00595 glutamate--ammonia ligase

Query= SwissProt::Q3V5W6
         (468 letters)



>NCBI__GCF_000967895.1:WP_046007614.1
          Length = 468

 Score =  701 bits (1810), Expect = 0.0
 Identities = 332/464 (71%), Positives = 396/464 (85%), Gaps = 1/464 (0%)

Query: 4   SVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEAS 63
           ++ LIK++DVKW+DLRFTDTKG +HHV++P+   ++++FFEVG+MFDGSSIAGWKGI  S
Sbjct: 5   TLNLIKENDVKWVDLRFTDTKGKEHHVSIPS-SYVDEEFFEVGQMFDGSSIAGWKGINES 63

Query: 64  DMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDT 123
           DMILLPDD T+ LDPFTED+TLIL CDIIEPSTMQGY+RDPR++A RAE +L+TTG+GDT
Sbjct: 64  DMILLPDDTTSFLDPFTEDSTLILRCDIIEPSTMQGYERDPRSVAKRAEAFLQTTGLGDT 123

Query: 124 VFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFPVP 183
            F GPEPEFFIFD+V++ +D+SG+ +KI SE+ +W S  +I GGN GHRP VKGGYFPVP
Sbjct: 124 AFFGPEPEFFIFDDVRWGADMSGNFYKINSEEAAWNSGAEIPGGNMGHRPTVKGGYFPVP 183

Query: 184 PFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVH 243
           P D  H++R AMCN +  +G  VEVHHHEVATA QNEIGVKFNTLVKKADEVQ LKYV+H
Sbjct: 184 PVDSSHDMRAAMCNTMMAIGLDVEVHHHEVATANQNEIGVKFNTLVKKADEVQMLKYVIH 243

Query: 244 NVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIK 303
           NVA AYG+TATFMPKP+ GDNGSGMHVH S  KDG+N FAG+ YAGLSE AL++IGGIIK
Sbjct: 244 NVAAAYGKTATFMPKPIIGDNGSGMHVHQSFWKDGENQFAGDSYAGLSEMALFYIGGIIK 303

Query: 304 HGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDP 363
           H KALN FTNP+TNSYKRL+PGFEAPVMLAYSARNRSASIRIPYV SP+G+RIEARFPDP
Sbjct: 304 HAKALNAFTNPSTNSYKRLIPGFEAPVMLAYSARNRSASIRIPYVASPKGKRIEARFPDP 363

Query: 364 AANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDK 423
            ANPYLAF+A+LMAG+DGI+NKIHPGDAADK+LYDLP EEA  IPQV GSL+EA++ L  
Sbjct: 364 MANPYLAFSAMLMAGIDGIKNKIHPGDAADKDLYDLPAEEAAAIPQVAGSLREAIDCLKA 423

Query: 424 GRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467
              FLT+GGVF++D I AYI L  E+  +V    HP+E+++YYS
Sbjct: 424 DSDFLTQGGVFTEDMIGAYIDLAMEDVYRVEQTTHPVEFDMYYS 467


Lambda     K      H
   0.318    0.137    0.409 

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: 787
Number of extensions: 29
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: 468
Length of database: 468
Length adjustment: 33
Effective length of query: 435
Effective length of database: 435
Effective search space:   189225
Effective search space used:   189225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_046007614.1 OLEAN_RS00595 (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.2216603.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-206  670.7   0.0     6e-206  670.5   0.0    1.0  1  NCBI__GCF_000967895.1:WP_046007614.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000967895.1:WP_046007614.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.5   0.0    6e-206    6e-206       4     462 .]       6     467 ..       3     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 670.5 bits;  conditional E-value: 6e-206
                             TIGR00653   4 lkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivP 76 
                                           l+l+ke++vk vdlrf+D+kGk+++v+ip s ++ee++e g +FDgss+ G+k+i+esD++l pd  t + +P
  NCBI__GCF_000967895.1:WP_046007614.1   6 LNLIKENDVKWVDLRFTDTKGKEHHVSIPSSYVDEEFFEVGQMFDGSSIAGWKGINESDMILLPDDTTSFLDP 78 
                                           6899********************************************************************* PP

                             TIGR00653  77 fraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflev 148
                                           f+++++l+++cd+ ep t++ yerdpRs+akrae  l+ t+lgd+++fGpE+EFf+fd+v+ +  ++ +f+++
  NCBI__GCF_000967895.1:WP_046007614.1  79 FTEDSTLILRCDIIEPSTMQGYERDPRSVAKRAEAFLQtTGLGDTAFFGPEPEFFIFDDVRWGADMSGNFYKI 151
                                           **************************************9********************************** PP

                             TIGR00653 149 dseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidik 218
                                           +see++wn  +e+++gn g++++ kggYf+v+pvD+ +d+r  +++++ ++gl+vev+HHEvata q+Ei++k
  NCBI__GCF_000967895.1:WP_046007614.1 152 NSEEAAWNsgAEIPGGNMGHRPTVKGGYFPVPPVDSSHDMRAAMCNTMMAIGLDVEVHHHEVATAnQNEIGVK 224
                                           ********99999************************************************************ PP

                             TIGR00653 219 fdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetaly 291
                                           f++lvk+aDe++++Kyv++nva+ +GktatFmpKp++gdngsGmHvh+s wkdgen fag++ yagLse+al+
  NCBI__GCF_000967895.1:WP_046007614.1 225 FNTLVKKADEVQMLKYVIHNVAAAYGKTATFMPKPIIGDNGSGMHVHQSFWKDGENQFAGDS-YAGLSEMALF 296
                                           **************************************************************.********** PP

                             TIGR00653 292 yigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYL 364
                                           yigGi+kHakal+A+tnp++nsYkRL+pG+EAPv+laysa+nRsa+iRiP++a+pk+kRiE R+pDp anpYL
  NCBI__GCF_000967895.1:WP_046007614.1 297 YIGGIIKHAKALNAFTNPSTNSYKRLIPGFEAPVMLAYSARNRSASIRIPYVASPKGKRIEARFPDPMANPYL 369
                                           ************************************************************************* PP

                             TIGR00653 365 afaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelie 435
                                           af+a+lmAg+dGiknki+pg++ dk+ly+l+ ee++   i+q++ sL+ea+d l++d+  +++++v++e++i 
  NCBI__GCF_000967895.1:WP_046007614.1 370 AFSAMLMAGIDGIKNKIHPGDAADKDLYDLPAEEAAA--IPQVAGSLREAIDCLKADSdfLTQGGVFTEDMIG 440
                                           ***********************************99..******************988999********** PP

                             TIGR00653 436 afielkrkEveelrlkvhpvElekyld 462
                                           a+i+l +++v +++ + hpvE+ +y++
  NCBI__GCF_000967895.1:WP_046007614.1 441 AYIDLAMEDVYRVEQTTHPVEFDMYYS 467
                                           *************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (468 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.94
//
[ok]

This GapMind analysis is from Jul 25 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:

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