Alignments for a candidate for glnA in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Haloechinothrix alba DSM 45207

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_089303133.1 CHB84_RS19600 type I glutamate--ammonia ligase

Query= BRENDA::O85177
         (466 letters)



>NCBI__GCF_900188115.1:WP_089303133.1
          Length = 430

 Score =  724 bits (1869), Expect = 0.0
 Identities = 339/424 (79%), Positives = 375/424 (88%)

Query: 4   TPDDIQRLIADEDVEVIDVQFCDLPGVMQHFTVPAKAFTEEAYEEGLAFDGSSVRGFQSI 63
           +P+D+   I+DE V+ IDV+FCDLPGVMQHFTVPA +F  E +  GLAFDGSSVRGFQ I
Sbjct: 4   SPEDLLSFISDEGVKFIDVRFCDLPGVMQHFTVPASSFDNETFTNGLAFDGSSVRGFQEI 63

Query: 64  HESDMLLLPDAATARIDPFRKAKTLALNFFVHDPFTREAYSRDPRNIARKAEQYIAEYGV 123
           HESDMLLLPD  TAR+DPFR  KTL +NFFVHDPFTRE YSRDPRNIA+KAE YIAE G+
Sbjct: 64  HESDMLLLPDPYTARLDPFRTEKTLMMNFFVHDPFTREPYSRDPRNIAKKAEDYIAESGI 123

Query: 124 ADNVYFGPEAEFYIFDSIRFDSAEHASFHEIDSVEGWWNTGADEVGGNQGYKTKFKGGYF 183
           AD  +FGPEAEFY+FDS+RF  +E+ASFHEIDS+EGWWNTG DE GGN+GYKT+FKGGYF
Sbjct: 124 ADLAFFGPEAEFYVFDSVRFSHSENASFHEIDSIEGWWNTGRDEEGGNRGYKTRFKGGYF 183

Query: 184 PVPPVDHFADLRDDIVRNLQGSGFEIERAHHEVGTAGQTEINYKFNTLLHAADDLQLFKY 243
           PVPPVDH+ADLRD I   L+ +G  +ERAHHEVGTAGQ EINYKFNTLLHA DDLQLFKY
Sbjct: 184 PVPPVDHYADLRDKISLKLEEAGLTVERAHHEVGTAGQAEINYKFNTLLHAGDDLQLFKY 243

Query: 244 IVKNTVFAAGKTATFMPKPLAGDNGSGMHCHQSLWKDGQPLFHDESGYAGLSDTARHYIG 303
           IVKNT +  GK+ATFMPKPL GDNGSGMHCHQSLWKDG PLFHDESGYAGLSDTARHYIG
Sbjct: 244 IVKNTAWEEGKSATFMPKPLFGDNGSGMHCHQSLWKDGVPLFHDESGYAGLSDTARHYIG 303

Query: 304 GLLKHAPSLLAFTNPTVNSYHRLVPGFEAPVSLVYSQRNRSACVRIPITGNNPKAKRAEF 363
           G+L HAPSLLAFTNPT+NSY RLVPGFEAPVSLVYSQRNRSACVRIPITG++PKAKR EF
Sbjct: 304 GILTHAPSLLAFTNPTINSYRRLVPGFEAPVSLVYSQRNRSACVRIPITGDSPKAKRIEF 363

Query: 364 RCPDSSGNPYLAFSAMMMAGLDGIRNKIEPPEPIDKDLYELPPEEAKDVKLVPGDLGTVL 423
           RCPDSSGNPYLAF+AM+MAG+DG+RNKIEPPEPIDKDLYELPPEE  DV  VPGDL +VL
Sbjct: 364 RCPDSSGNPYLAFAAMLMAGIDGVRNKIEPPEPIDKDLYELPPEEQADVAQVPGDLNSVL 423

Query: 424 NTLE 427
           + LE
Sbjct: 424 DNLE 427


Lambda     K      H
   0.319    0.138    0.422 

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: 836
Number of extensions: 29
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: 466
Length of database: 430
Length adjustment: 33
Effective length of query: 433
Effective length of database: 397
Effective search space:   171901
Effective search space used:   171901
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_089303133.1 CHB84_RS19600 (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.2203915.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-195  636.2   0.0   1.6e-195  636.1   0.0    1.0  1  NCBI__GCF_900188115.1:WP_089303133.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188115.1:WP_089303133.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  636.1   0.0  1.6e-195  1.6e-195       2     422 ..       7     430 .]       6     430 .] 0.99

  Alignments for each domain:
  == domain 1  score: 636.1 bits;  conditional E-value: 1.6e-195
                             TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 
                                           ++l+++ +e vkf+d+rf+D+ G+++++++p+s++++e++++g+aFDgssv+Gf++i+esD+ll pdp t+  
  NCBI__GCF_900188115.1:WP_089303133.1   7 DLLSFISDEGVKFIDVRFCDLPGVMQHFTVPASSFDNETFTNGLAFDGSSVRGFQEIHESDMLLLPDPYTARL 79 
                                           5678899****************************************************************** PP

                             TIGR00653  75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146
                                           +Pfr+ek+l++++ v++p+t+epy+rdpR+iak+ae+++  ++++d ++fGpEaEF++fd+v+f++++n+sf 
  NCBI__GCF_900188115.1:WP_089303133.1  80 DPFRTEKTLMMNFFVHDPFTREPYSRDPRNIAKKAEDYIAeSGIADLAFFGPEAEFYVFDSVRFSHSENASFH 152
                                           ***************************************999******************************* PP

                             TIGR00653 147 evdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEid 216
                                           e+ds+eg+wn  r++e+gn+gyk++ kggYf+v+pvD++ d+r+++ l+lee gl+ve  HHEv+ta qaEi+
  NCBI__GCF_900188115.1:WP_089303133.1 153 EIDSIEGWWNtgRDEEGGNRGYKTRFKGGYFPVPPVDHYADLRDKISLKLEEAGLTVERAHHEVGTAgQAEIN 225
                                           **********9999999******************************************************** PP

                             TIGR00653 217 ikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLseta 289
                                           +kf++l++a+D+++l+Ky+vkn+a+++Gk atFmpKplfgdngsGmH+h+slwkdg +lf++e+gyagLs+ta
  NCBI__GCF_900188115.1:WP_089303133.1 226 YKFNTLLHAGDDLQLFKYIVKNTAWEEGKSATFMPKPLFGDNGSGMHCHQSLWKDGVPLFHDESGYAGLSDTA 298
                                           ************************************************************************* PP

                             TIGR00653 290 lyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasa.npkakRiEvRspDpsan 361
                                           ++yigGil Ha++l A+tnpt+nsY+RLvpG+EAPv l+ys++nRsa++RiP++  +pkakRiE+R+pD+s+n
  NCBI__GCF_900188115.1:WP_089303133.1 299 RHYIGGILTHAPSLLAFTNPTINSYRRLVPGFEAPVSLVYSQRNRSACVRIPITGdSPKAKRIEFRCPDSSGN 371
                                           *******************************************************9***************** PP

                             TIGR00653 362 pYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk 422
                                           pYLafaa+lmAg+dG++nki+p+ep+dk+lyel++ee+++  + q+p +L+ +ld+le+d+
  NCBI__GCF_900188115.1:WP_089303133.1 372 PYLAFAAMLMAGIDGVRNKIEPPEPIDKDLYELPPEEQAD--VAQVPGDLNSVLDNLERDH 430
                                           ****************************************..*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (430 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: 19.52
//
[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