Alignments for a candidate for glnA in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Ferroglobus placidus DSM 10642

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_012966150.1 FERP_RS08330 type I glutamate--ammonia ligase

Query= BRENDA::O29313
         (491 letters)



>NCBI__GCF_000025505.1:WP_012966150.1
          Length = 480

 Score =  829 bits (2141), Expect = 0.0
 Identities = 385/479 (80%), Positives = 435/479 (90%), Gaps = 2/479 (0%)

Query: 14  ERAKAVLKENNVRQVLCAFADVRGYLQMFSIPAREFVDGSAFENGIGFDGSSVRGFRTIE 73
           E  + +L+EN V+QVLCAF DVRGYL  FSIPAREF++G+ F+ GIGFDGSS+RGF+TIE
Sbjct: 3   EEVRKILEENGVKQVLCAFTDVRGYLMTFSIPAREFIEGNTFD-GIGFDGSSIRGFKTIE 61

Query: 74  KSDMVWMPDASSLKIIPWIDDPIQKSAIMFGNVYEAWGTEIADCDPRGYVAKRYEDMLKS 133
           +SDMVWMPD  +L++IPW +DP+QKSAIMFG+VYEAW  E ADCDPRGYVAKR E  LK 
Sbjct: 62  QSDMVWMPDPKTLRVIPWENDPLQKSAIMFGDVYEAWAAEQADCDPRGYVAKRMEKQLKD 121

Query: 134 EGMSAIFGPEIEFFLFEGVDFTRLSWDMWVSPNGGAGDSWGPPRIMPISSELESG-YMIR 192
           +G+S IFGPEIEFFLFE +D TRL WD+WVSPNGGAGDSWGPPR+MP S ELE+G Y+IR
Sbjct: 122 KGLSVIFGPEIEFFLFEKIDPTRLYWDLWVSPNGGAGDSWGPPRVMPESRELEAGWYVIR 181

Query: 193 PKEGYFRPPPEDTTVEYRNELVYYLEQLGIDIEYHHHEVATAGQVELDFKPKQLVDVGDA 252
           PKEGYFRPPPEDTTV YRNELV+YLE+LGI +EYHHHEVATAGQVELDFKP QLVDV DA
Sbjct: 182 PKEGYFRPPPEDTTVAYRNELVHYLEKLGIIVEYHHHEVATAGQVELDFKPMQLVDVSDA 241

Query: 253 FYLYKFAAKNIAAMHGLYATFMPKPLYLDNASGMHTHQSLWKGEPFSGEAVFADPDDEYM 312
           FYLYKFAAKN+AA+HG+ A FMPKPLYLDNASGMH HQSLW+GEPF G+ +FADPDDE+M
Sbjct: 242 FYLYKFAAKNVAALHGMMAVFMPKPLYLDNASGMHVHQSLWEGEPFKGKNIFADPDDEFM 301

Query: 313 LSQKARYYIGGLLEHAKALTALCAPTVNSYKRLVPGFEAPIYICWSPRNRSALVRVPMYV 372
           LSQKARYYIGGLLEHAKALTALCAPT+NSYKRLVPGFEAPIYICWSPRNRSALVRVPMY 
Sbjct: 302 LSQKARYYIGGLLEHAKALTALCAPTINSYKRLVPGFEAPIYICWSPRNRSALVRVPMYH 361

Query: 373 KKPSAIRVEYRGVDPSCNPYLAITAQLAAGLDGIKKKIDPGDPLLEDVYELTPAQKRELG 432
           +KPSAIRVEYRG DPS NPYL++ A +AAGLDGIKKKIDPGDP++EDVYEL+ +QKRELG
Sbjct: 362 RKPSAIRVEYRGADPSTNPYLSLAAMVAAGLDGIKKKIDPGDPIMEDVYELSESQKRELG 421

Query: 433 VGELPTTLRDAIDHLASDELMQEVLGSHIFDAFMELKIDEWNQYCLYITPWEFMKYFDI 491
           +GELPTTLRDA+DHLA+DE++Q+VLGSHIFDAFM +KIDEWNQYCLYITPWE MKY DI
Sbjct: 422 IGELPTTLRDALDHLATDEVIQKVLGSHIFDAFMSIKIDEWNQYCLYITPWEIMKYLDI 480


Lambda     K      H
   0.321    0.139    0.433 

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: 979
Number of extensions: 31
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: 491
Length of database: 480
Length adjustment: 34
Effective length of query: 457
Effective length of database: 446
Effective search space:   203822
Effective search space used:   203822
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_012966150.1 FERP_RS08330 (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.6154.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-192  623.9   0.0   9.1e-192  623.7   0.0    1.0  1  lcl|NCBI__GCF_000025505.1:WP_012966150.1  FERP_RS08330 type I glutamate--a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025505.1:WP_012966150.1  FERP_RS08330 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.7   0.0  9.1e-192  9.1e-192       1     462 []       3     479 ..       3     479 .. 0.97

  Alignments for each domain:
  == domain 1  score: 623.7 bits;  conditional E-value: 9.1e-192
                                 TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdp 69 
                                               eev k+l+e+ vk+v ++f+D++G+l +++ip++e+ e    +gi FDgss++Gfk+ie+sD++++pdp
  lcl|NCBI__GCF_000025505.1:WP_012966150.1   3 EEVRKILEENGVKQVLCAFTDVRGYLMTFSIPAREFIEGNTFDGIGFDGSSIRGFKTIEQSDMVWMPDP 71 
                                               578999*******************************99999*************************** PP

                                 TIGR00653  70 etlvivPfraek...vlrvicdvyepvtkepyerdpR.siakraeeelktklgdevyfGpEaEFflfdk 134
                                               +tl ++P+++++   ++++++dvye++  e++++dpR ++akr+e++lk + g +v+fGpE+EFflf+k
  lcl|NCBI__GCF_000025505.1:WP_012966150.1  72 KTLRVIPWENDPlqkSAIMFGDVYEAWAAEQADCDPRgYVAKRMEKQLK-DKGLSVIFGPEIEFFLFEK 139
                                               **********988889*********************99*********7.8999*************** PP

                                 TIGR00653 135 vefkeasnssflevdseege.wn..reveeg....nkgykikkkggYfdvepvDkakdirrelvlalee 196
                                               ++ ++  ++ +++ +  +g+ w+  r ++e+       y i+ k+gYf+++p+D+++ +r+elv++le+
  lcl|NCBI__GCF_000025505.1:WP_012966150.1 140 IDPTRLYWDLWVSPNGGAGDsWGppRVMPESreleAGWYVIRPKEGYFRPPPEDTTVAYRNELVHYLEK 208
                                               ******************988***98888886663345899**************************** PP

                                 TIGR00653 197 lglevevsHHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHv 264
                                               lg+ ve++HHEvata q+E+d+k  +lv+++D+++lyK+++knva+ hG +a FmpKpl+ dn+sGmHv
  lcl|NCBI__GCF_000025505.1:WP_012966150.1 209 LGIIVEYHHHEVATAgQVELDFKPMQLVDVSDAFYLYKFAAKNVAALHGMMAVFMPKPLYLDNASGMHV 277
                                               ********************************************************************* PP

                                 TIGR00653 265 hlslwk....dgenlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylay 329
                                               h+slw+    +g+n+fa++++   Ls++a+yyigG+l+Hakal+Al++pt+nsYkRLvpG+EAP+y+++
  lcl|NCBI__GCF_000025505.1:WP_012966150.1 278 HQSLWEgepfKGKNIFADPDDEFMLSQKARYYIGGLLEHAKALTALCAPTINSYKRLVPGFEAPIYICW 346
                                               *****999999**********777********************************************* PP

                                 TIGR00653 330 saknRsaliRiPasa.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelsee 397
                                               s +nRsal+R+P++  +p+a+R+E+R  Dps+npYL++aa+++AgldGik+kidpg+p+ +++yelse+
  lcl|NCBI__GCF_000025505.1:WP_012966150.1 347 SPRNRSALVRVPMYHrKPSAIRVEYRGADPSTNPYLSLAAMVAAGLDGIKKKIDPGDPIMEDVYELSES 415
                                               **************99***************************************************** PP

                                 TIGR00653 398 elkelGieqlpesLeealdelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               +++elGi +lp++L++ald+l++d ev+++vlg+++++af+++k +E+++++l+++p+E++kyld
  lcl|NCBI__GCF_000025505.1:WP_012966150.1 416 QKRELGIGELPTTLRDALDHLATD-EVIQKVLGSHIFDAFMSIKIDEWNQYCLYITPWEIMKYLD 479
                                               ************************.**************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (480 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.15
//
[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