Alignments for a candidate for glnA in Frankia alni ACN14A

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Frankia alni ACN14A

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011606265.1 FRAAL_RS22510 type I glutamate--ammonia ligase

Query= BRENDA::O85177
         (466 letters)



>NCBI__GCF_000058485.1:WP_011606265.1
          Length = 474

 Score =  670 bits (1728), Expect = 0.0
 Identities = 312/474 (65%), Positives = 373/474 (78%), Gaps = 8/474 (1%)

Query: 1   MPTTPDDIQRLIADEDVEVIDVQFCDLPGVMQHFTVPAKAFTEEAYEEGLAFDGSSVRGF 60
           M T  +D+ R I DEDV+ IDV+FCDLPG+MQHFT+P + F E  + +GL FDGSS+RGF
Sbjct: 1   MFTKAEDVLRYIRDEDVQFIDVRFCDLPGIMQHFTIPTQVFAESVFTDGLMFDGSSIRGF 60

Query: 61  QSIHESDMLLLPDAATARIDPFRKAKTLALNFFVHDPFTREAYSRDPRNIARKAEQYIAE 120
           Q+IHESDMLLLPD  TA +DPFR+ KTLA+ FF+HDP T+E YSRDPRNIA+KAE Y+  
Sbjct: 61  QAIHESDMLLLPDPQTAFVDPFREHKTLAMTFFIHDPITKEQYSRDPRNIAKKAETYLRG 120

Query: 121 YGVADNVYFGPEAEFYIFDSIRFDSAEHASFHEIDSVEGWWNTGADEVGGNQGYKTKFKG 180
            G+AD  YFGPEAEFYIFD +R+D   + S H++DSVE  WNT   E GGN GYK +FKG
Sbjct: 121 TGIADTAYFGPEAEFYIFDDVRYDYNPYGSMHQVDSVEAAWNTSRKEEGGNLGYKPRFKG 180

Query: 181 GYFPVPPVDHFADLRDDIVRNLQGSGFEIERAHHEVGTAGQTEINYKFNTLLHAADDLQL 240
           GYFPVPP DHF DLR ++ R L  +G  +E  HHEVGTAGQ EI+ +++TLL  AD+L L
Sbjct: 181 GYFPVPPTDHFTDLRSEMTRVLYETGITVEMQHHEVGTAGQAEIDIRYDTLLKTADNLML 240

Query: 241 FKYIVKNTVFAAGKTATFMPKPLAGDNGSGMHCHQSLWKDGQPLFHDESGYAGLSDTARH 300
           +KY+++N   + GKT TFMPKPL  DNGSGMH H SLWKDG+PLF+  +GY GLSDTAR+
Sbjct: 241 YKYVIRNVARSRGKTVTFMPKPLFEDNGSGMHVHSSLWKDGEPLFYSPNGYGGLSDTARY 300

Query: 301 YIGGLLKHAPSLLAFTNPTVNSYHRLVPGFEAPVSLVYSQRNRSACVRIPITGNNPKAKR 360
           YIGGLL HAP+LLAFTNPT NSY RLVPG+EAPV+LVYS RNRSAC RIP+ G++PKAKR
Sbjct: 301 YIGGLLHHAPALLAFTNPTTNSYRRLVPGYEAPVNLVYSARNRSACCRIPLGGDSPKAKR 360

Query: 361 AEFRCPDSSGNPYLAFSAMMMAGLDGIRNKIEPPEPIDKDLYELPPEEAKDVKLVPGDLG 420
            EFR PD S NPYLAF+AM+MAGLDGIRNKI+PP+PIDKDLYELPP+E   V  VPG L 
Sbjct: 361 VEFRVPDPSCNPYLAFAAMLMAGLDGIRNKIDPPDPIDKDLYELPPDELAAVPQVPGSLE 420

Query: 421 TVLNTL--------EGGVFTPDVIETWISYKRENEIDPLRLRPHPYEFSLYYDV 466
            VL+ L        EG VFT D+IETW+ YKR NE+D +RLRPHPYEF+LYYD+
Sbjct: 421 KVLDALEADNDFLREGDVFTTDLIETWLEYKRLNEVDAIRLRPHPYEFTLYYDI 474


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: 862
Number of extensions: 38
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: 466
Length of database: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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_011606265.1 FRAAL_RS22510 (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.27525.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-210  684.1   0.0     5e-210  683.9   0.0    1.0  1  lcl|NCBI__GCF_000058485.1:WP_011606265.1  FRAAL_RS22510 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_011606265.1  FRAAL_RS22510 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.9   0.0    5e-210    5e-210       1     462 []       6     473 ..       6     473 .. 0.99

  Alignments for each domain:
  == domain 1  score: 683.9 bits;  conditional E-value: 5e-210
                                 TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdp 69 
                                               e+vl+++++e+v+f+d+rf+D+ G++++++ip + + e+++++g++FDgss++Gf++i+esD+ll pdp
  lcl|NCBI__GCF_000058485.1:WP_011606265.1   6 EDVLRYIRDEDVQFIDVRFCDLPGIMQHFTIPTQVFAESVFTDGLMFDGSSIRGFQAIHESDMLLLPDP 74 
                                               5788999************************************************************** PP

                                 TIGR00653  70 etlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvef 137
                                               +t++++Pfr++k+l +++ +++p+tke+y+rdpR+iak+ae +l+ t+++d++yfGpEaEF++fd+v+ 
  lcl|NCBI__GCF_000058485.1:WP_011606265.1  75 QTAFVDPFREHKTLAMTFFIHDPITKEQYSRDPRNIAKKAETYLRgTGIADTAYFGPEAEFYIFDDVRY 143
                                               ********************************************************************* PP

                                 TIGR00653 138 keasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevs 204
                                               + +   s+ +vds+e++wn  r++e+gn gyk++ kggYf+v+p+D+ +d+r+e++ +l e g++ve++
  lcl|NCBI__GCF_000058485.1:WP_011606265.1 144 DYNPYGSMHQVDSVEAAWNtsRKEEGGNLGYKPRFKGGYFPVPPTDHFTDLRSEMTRVLYETGITVEMQ 212
                                               *******************99999999****************************************** PP

                                 TIGR00653 205 HHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdg 272
                                               HHEv+ta qaEidi++d+l+k+aD+++lyKyv++nva+  Gkt+tFmpKplf dngsGmHvh slwkdg
  lcl|NCBI__GCF_000058485.1:WP_011606265.1 213 HHEVGTAgQAEIDIRYDTLLKTADNLMLYKYVIRNVARSRGKTVTFMPKPLFEDNGSGMHVHSSLWKDG 281
                                               ********************************************************************* PP

                                 TIGR00653 273 enlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiP 341
                                               e+lf+ ++gy gLs+ta+yyigG+l+Ha+al A+tnpt+nsY+RLvpGyEAPv+l+ysa+nRsa+ RiP
  lcl|NCBI__GCF_000058485.1:WP_011606265.1 282 EPLFYSPNGYGGLSDTARYYIGGLLHHAPALLAFTNPTTNSYRRLVPGYEAPVNLVYSARNRSACCRIP 350
                                               ********************************************************************* PP

                                 TIGR00653 342 asa.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpe 409
                                               +   +pkakR+E+R+pDps+npYLafaa+lmAgldGi+nkidp++p+dk+lyel+++el+   ++q+p 
  lcl|NCBI__GCF_000058485.1:WP_011606265.1 351 LGGdSPKAKRVEFRVPDPSCNPYLAFAAMLMAGLDGIRNKIDPPDPIDKDLYELPPDELAA--VPQVPG 417
                                               **99********************************************************9..****** PP

                                 TIGR00653 410 sLeealdelesdk..evlkevlgeelieafielkr.kEveelrlkvhpvElekyld 462
                                               sLe++ld+le+d+  + +++v++++lie+++e+kr +Ev+ +rl++hp+E++ y+d
  lcl|NCBI__GCF_000058485.1:WP_011606265.1 418 SLEKVLDALEADNdfLREGDVFTTDLIETWLEYKRlNEVDAIRLRPHPYEFTLYYD 473
                                               *************8888999**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (474 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: 12.52
//
[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