Alignments for a candidate for glnA in Methylocapsa acidiphila B2

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methylocapsa acidiphila B2

Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_026606401.1 METAC_RS0106470 type I glutamate--ammonia ligase

Query= CharProtDB::CH_024014
         (469 letters)



>NCBI__GCF_000427445.1:WP_026606401.1
          Length = 469

 Score =  608 bits (1569), Expect = e-179
 Identities = 295/467 (63%), Positives = 356/467 (76%), Gaps = 1/467 (0%)

Query: 2   SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61
           +A+ VL  + ++++K+VD RFTD +GK QHVT     +  E F EG MFDGSSI GWK I
Sbjct: 3   TAKDVLKSIKDNDIKYVDFRFTDPRGKWQHVTFDVSLIEDETFTEGVMFDGSSIAGWKAI 62

Query: 62  NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTGI 121
           NESDM L+PD  TA IDPFFA  TL+I CDIL+P + + Y RDPR IAK+AE +  S+GI
Sbjct: 63  NESDMTLLPDPKTAFIDPFFAAPTLVIVCDILDPASGEPYSRDPRGIAKKAEAFAASSGI 122

Query: 122 ADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGYF 181
           AD   FGPE EFF+FDD+RF +        +D  E   N+ T YEGGN GHR   KGGYF
Sbjct: 123 ADAAYFGPEAEFFVFDDVRFNTDPYNMGFILDSSELPSNTGTPYEGGNLGHRIRTKGGYF 182

Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241
           PVPP DSAQD+R EM   M QMG  VE HHHEVA+A Q+E+  +F  +T  AD +QIYKY
Sbjct: 183 PVPPQDSAQDMRGEMLAAMAQMGAKVEKHHHEVASA-QHELGLKFGPLTTMADHLQIYKY 241

Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGG 301
            +H VAH +GK+ATFMPKP+FGDNGSGMH H SL K G  LFAG+KYA LSE+ L+YIGG
Sbjct: 242 AIHQVAHSYGKSATFMPKPIFGDNGSGMHVHQSLWKGGKPLFAGNKYADLSEECLFYIGG 301

Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRF 361
           +I+HA+A+NA  NP+TNSYKRLVPGYEAPV+LAYSARNRSAS RIP  ++PKA+R+EVRF
Sbjct: 302 IIRHARALNAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFATNPKAKRVEVRF 361

Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNE 421
           PDPAANPYL FAA+L+AG+DGI NKI PG AMDK+LYDLPP+E K+IP V GSL EAL+ 
Sbjct: 362 PDPAANPYLAFAAMLLAGIDGILNKIDPGAAMDKDLYDLPPKELKKIPTVCGSLREALSN 421

Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468
           LD DR FLKAGGVF D+ ID+YI L+ ++  R   TPHPVEF++YYS
Sbjct: 422 LDKDRAFLKAGGVFDDDFIDSYIDLKMQDVLRFETTPHPVEFDMYYS 468


Lambda     K      H
   0.318    0.136    0.400 

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: 773
Number of extensions: 28
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: 469
Length of database: 469
Length adjustment: 33
Effective length of query: 436
Effective length of database: 436
Effective search space:   190096
Effective search space used:   190096
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_026606401.1 METAC_RS0106470 (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.2192849.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-199  647.4   0.0   6.6e-199  647.3   0.0    1.0  1  NCBI__GCF_000427445.1:WP_026606401.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000427445.1:WP_026606401.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.3   0.0  6.6e-199  6.6e-199       2     462 .]       6     468 ..       5     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 647.3 bits;  conditional E-value: 6.6e-199
                             TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 
                                           +vlk +k++++k+vd+rf+D +Gk+++v++ vs +e+e+++eg++FDgss+ G+k+i+esD+ l pdp+t++i
  NCBI__GCF_000427445.1:WP_026606401.1   6 DVLKSIKDNDIKYVDFRFTDPRGKWQHVTFDVSLIEDETFTEGVMFDGSSIAGWKAINESDMTLLPDPKTAFI 78 
                                           68999******************************************************************** PP

                             TIGR00653  75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146
                                           +Pf a+++l+++cd+ +p+ +epy+rdpR iak+ae     ++++d +yfGpEaEFf+fd+v+f++   ++ +
  NCBI__GCF_000427445.1:WP_026606401.1  79 DPFFAAPTLVIVCDILDPASGEPYSRDPRGIAKKAEAFAAsSGIADAAYFGPEAEFFVFDDVRFNTDPYNMGF 151
                                           *************************************99989******************************* PP

                             TIGR00653 147 evdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidi 217
                                            +ds e   n  + +e+gn g++i++kggYf+v+p+D+a+d+r e++ a++++g +ve++HHEva+aq+E+++
  NCBI__GCF_000427445.1:WP_026606401.1 152 ILDSSELPSNtgTPYEGGNLGHRIRTKGGYFPVPPQDSAQDMRGEMLAAMAQMGAKVEKHHHEVASAQHELGL 224
                                           ****99888877889999******************************************************* PP

                             TIGR00653 218 kfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetal 290
                                           kf  l+++aD++++yKy++++va+ +Gk atFmpKp+fgdngsGmHvh+slwk g++lfag++ ya+Lse++l
  NCBI__GCF_000427445.1:WP_026606401.1 225 KFGPLTTMADHLQIYKYAIHQVAHSYGKSATFMPKPIFGDNGSGMHVHQSLWKGGKPLFAGNK-YADLSEECL 296
                                           ***************************************************************.********* PP

                             TIGR00653 291 yyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpY 363
                                           +yigGi++Ha+al+A+tnp++nsYkRLvpGyEAPv laysa+nRsa+ RiP ++npkakR+EvR+pDp+anpY
  NCBI__GCF_000427445.1:WP_026606401.1 297 FYIGGIIRHARALNAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFATNPKAKRVEVRFPDPAANPY 369
                                           ************************************************************************* PP

                             TIGR00653 364 LafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeeli 434
                                           Lafaa+l Ag+dGi nkidpg+++dk+ly+l+++elk+  i+++  sL+eal +l++d+  +++++v+ +++i
  NCBI__GCF_000427445.1:WP_026606401.1 370 LAFAAMLLAGIDGILNKIDPGAAMDKDLYDLPPKELKK--IPTVCGSLREALSNLDKDRafLKAGGVFDDDFI 440
                                           **************************************..*******************99999********* PP

                             TIGR00653 435 eafielkrkEveelrlkvhpvElekyld 462
                                           +++i+lk+++v ++++++hpvE+ +y++
  NCBI__GCF_000427445.1:WP_026606401.1 441 DSYIDLKMQDVLRFETTPHPVEFDMYYS 468
                                           **************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (469 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.69
//
[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