Alignments for a candidate for glnA in Rhizobium leguminosarum 3841

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Rhizobium leguminosarum 3841

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011651961.1 RL_RS12340 type I glutamate--ammonia ligase

Query= BRENDA::P0A1P6
         (469 letters)



>NCBI__GCF_000009265.1:WP_011651961.1
          Length = 469

 Score =  637 bits (1644), Expect = 0.0
 Identities = 308/467 (65%), Positives = 372/467 (79%), Gaps = 1/467 (0%)

Query: 2   SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61
           +A  +L  + E++VKFVDLRFTD KGK QHVT+    V+ + F +G MFDGSSIGGWK I
Sbjct: 3   TASEILKQIKENDVKFVDLRFTDPKGKLQHVTMDVVCVDEDMFADGVMFDGSSIGGWKAI 62

Query: 62  NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGI 121
           NESDMVLMPD  T  +DPFFA ST++I CDIL+P + + Y+RDPR  AK+AE YL+A+GI
Sbjct: 63  NESDMVLMPDTETVHMDPFFAQSTMVIVCDILDPVSGEAYNRDPRGTAKKAEAYLKASGI 122

Query: 122 ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYF 181
            DTV  GPE EFF+FDD+++ A    +   +D  E   N  T YE GN GHRP VKGGYF
Sbjct: 123 GDTVFVGPEAEFFVFDDVKYKADPYNTGFKLDSTELPSNDDTDYETGNLGHRPRVKGGYF 182

Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241
           PVPPVDSAQD+RSEM  V+ +MG+VVE HHHEVA A Q+E+  +F+T+ + AD++QIYKY
Sbjct: 183 PVPPVDSAQDMRSEMLTVLSEMGVVVEKHHHEVAAA-QHELGIKFDTLVRNADKMQIYKY 241

Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGG 301
           VVH VA+ +GKTATFMPKP+FGDNGSGMH H S+ K G   F+GD+YAGLSE  L+YIGG
Sbjct: 242 VVHQVANAYGKTATFMPKPIFGDNGSGMHVHQSIWKGGKPTFAGDEYAGLSESCLFYIGG 301

Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRF 361
           +IKHAKAINA  NP+TNSYKRLVPGYEAPV+LAYSARNRSAS RIP  ++PKA+R+EVRF
Sbjct: 302 IIKHAKAINAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFGSNPKAKRVEVRF 361

Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNA 421
           PDP ANPYL FAA+LMAGLDGIKNKIHPG+AMDK+LYDLPP+E K+IP V GSL EAL +
Sbjct: 362 PDPTANPYLAFAAMLMAGLDGIKNKIHPGKAMDKDLYDLPPKELKKIPTVCGSLREALES 421

Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468
           LD DR+FL AGGVF D+ IDA+I L+  E  R  MTPHPVE+++YYS
Sbjct: 422 LDKDRKFLTAGGVFDDDQIDAFIELKMAEVMRFEMTPHPVEYDMYYS 468


Lambda     K      H
   0.318    0.136    0.401 

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: 785
Number of extensions: 24
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_011651961.1 RL_RS12340 (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.28572.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-207  674.2   0.0   5.1e-207  674.0   0.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011651961.1  RL_RS12340 type I glutamate--amm


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011651961.1  RL_RS12340 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.0   0.0  5.1e-207  5.1e-207       2     462 .]       6     468 ..       5     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 674.0 bits;  conditional E-value: 5.1e-207
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               e+lk +ke++vkfvdlrf+D kGkl++v++ v  ++e+++ +g++FDgss+ G+k+i+esD++l+pd+e
  lcl|NCBI__GCF_000009265.1:WP_011651961.1   6 EILKQIKENDVKFVDLRFTDPKGKLQHVTMDVVCVDEDMFADGVMFDGSSIGGWKAINESDMVLMPDTE 74 
                                               68899**************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t+ ++Pf a+++++++cd+ +pv +e y+rdpR +ak+ae +lk +++gd+v++GpEaEFf+fd+v+ k
  lcl|NCBI__GCF_000009265.1:WP_011651961.1  75 TVHMDPFFAQSTMVIVCDILDPVSGEAYNRDPRGTAKKAEAYLKaSGIGDTVFVGPEAEFFVFDDVKYK 143
                                               ********************************************9************************ PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                                   ++ +++ds+e   n  +++e+gn g++++ kggYf+v+pvD+a+d+r+e++++l+e+g+ ve++H
  lcl|NCBI__GCF_000009265.1:WP_011651961.1 144 ADPYNTGFKLDSTELPSNddTDYETGNLGHRPRVKGGYFPVPPVDSAQDMRSEMLTVLSEMGVVVEKHH 212
                                               **************988878999********************************************** PP

                                 TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               HEva aq+E++ikfd+lv++aD++++yKyvv++va+ +GktatFmpKp+fgdngsGmHvh+s+wk g++
  lcl|NCBI__GCF_000009265.1:WP_011651961.1 213 HEVAAAQHELGIKFDTLVRNADKMQIYKYVVHQVANAYGKTATFMPKPIFGDNGSGMHVHQSIWKGGKP 281
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                                fag+e yagLse +l+yigGi+kHaka++A+tnp++nsYkRLvpGyEAPv laysa+nRsa+ RiP  
  lcl|NCBI__GCF_000009265.1:WP_011651961.1 282 TFAGDE-YAGLSESCLFYIGGIIKHAKAINAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFG 349
                                               ******.************************************************************** PP

                                 TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412
                                               +npkakR+EvR+pDp+anpYLafaa+lmAgldGiknki+pg+++dk+ly+l+++elk+  i+++  sL+
  lcl|NCBI__GCF_000009265.1:WP_011651961.1 350 SNPKAKRVEVRFPDPTANPYLAFAAMLMAGLDGIKNKIHPGKAMDKDLYDLPPKELKK--IPTVCGSLR 416
                                               **********************************************************..********* PP

                                 TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               eal++l++d+  +++++v+ ++ i+afielk++Ev ++++++hpvE  +y++
  lcl|NCBI__GCF_000009265.1:WP_011651961.1 417 EALESLDKDRkfLTAGGVFDDDQIDAFIELKMAEVMRFEMTPHPVEYDMYYS 468
                                               **********99999***********************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.20
//
[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