Alignments for a candidate for glnA in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Geobacter lovleyi SZ

Align glutamine synthetase, type I (characterized)
to candidate WP_012469935.1 GLOV_RS09325 type I glutamate--ammonia ligase

Query= metacyc::SYNPCC7942_2156-MONOMER
         (473 letters)



>NCBI__GCF_000020385.1:WP_012469935.1
          Length = 470

 Score =  640 bits (1652), Expect = 0.0
 Identities = 301/469 (64%), Positives = 373/469 (79%), Gaps = 1/469 (0%)

Query: 4   TAQEVLQLIQEKGIQLVDLKFIDMPGIWQHLTLHVSQIDENSFVEGVPFDGSSIRGWKAI 63
           T ++V++  +E G  +VD KF+D  G WQH+++ +++ DE++F EG  FDGSSIRGW+ I
Sbjct: 2   TPKQVVEFAKENGALMVDYKFMDFVGTWQHVSVPITEFDEDTFEEGQGFDGSSIRGWQPI 61

Query: 64  NESDMTMVPDPTTAWIDPFMKEPTLSMICTIYEPRTNTPYERCPRAIAQKAVDYLKASGI 123
           + SDM ++PDPT+A +DPF+  PTLS+IC I++P T   Y R PR IA+KA  YLK++GI
Sbjct: 62  HASDMILLPDPTSAKMDPFVAVPTLSLICNIFDPITKEDYTRDPRNIARKAEAYLKSTGI 121

Query: 124 GDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREEEGGNLGYKPRYKEGYF 183
           GDTA+FGPEAEFFIFD+VR+D   N+++Y VDS+EG WN+GREE   NLGYKPR+KEGYF
Sbjct: 122 GDTAFFGPEAEFFIFDEVRYDSTANQAFYMVDSVEGAWNTGREEFP-NLGYKPRHKEGYF 180

Query: 184 PVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLMTYKY 243
           P +P D+  D+R+EM++ +   G+ +E  HHEVATGGQ E+  RF  L++ AD L  +KY
Sbjct: 181 PCSPVDSQNDLRNEMVMELQKVGIRVECQHHEVATGGQAEIDMRFSSLVDMADQLQWFKY 240

Query: 244 VIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWNDGQPLFAGDQYAGLSQMALWYIGG 303
           VIKNV  R GKT+TFMPKPL+ DNGSGMH HQSIW DGQ LFAGD+Y GLSQMALWYIGG
Sbjct: 241 VIKNVAYRNGKTVTFMPKPLYGDNGSGMHCHQSIWKDGQNLFAGDKYGGLSQMALWYIGG 300

Query: 304 ILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNPKAKRLEFR 363
           I+KHA AL A+TNPTTNSYKRLVPGFEAPVN+AYS  NRSAS+RIP+  TNPKAKR+E+R
Sbjct: 301 IIKHAKALCAITNPTTNSYKRLVPGFEAPVNMAYSSRNRSASLRIPMMSTNPKAKRVEYR 360

Query: 364 CPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTPGSLKDALK 423
            PD + N YLAFAAML AG+DGI+N+IDPG+PLD DIY LSPEEL  IPS PGSL +ALK
Sbjct: 361 TPDPSCNGYLAFAAMLMAGLDGIENKIDPGQPLDKDIYGLSPEELKDIPSAPGSLDEALK 420

Query: 424 ALEADHDFLTVGGVFTEDFIQNWIEYKLDNEVIPISLRPHPYEFALYYD 472
            LEADH+FL  G VFT D I+ WIEYK++ EV P+ +RP P EFALYYD
Sbjct: 421 CLEADHEFLLKGDVFTPDVIEKWIEYKMEAEVNPVRMRPVPLEFALYYD 469


Lambda     K      H
   0.319    0.138    0.428 

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: 30
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: 473
Length of database: 470
Length adjustment: 33
Effective length of query: 440
Effective length of database: 437
Effective search space:   192280
Effective search space used:   192280
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_012469935.1 GLOV_RS09325 (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.22933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-210  683.7   0.0   6.7e-210  683.5   0.0    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012469935.1  GLOV_RS09325 type I glutamate--a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012469935.1  GLOV_RS09325 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.5   0.0  6.7e-210  6.7e-210       2     462 .]       5     469 ..       4     469 .. 0.98

  Alignments for each domain:
  == domain 1  score: 683.5 bits;  conditional E-value: 6.7e-210
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +v++++ke+   +vd +f+D  G++++v++p++e++e+++eeg  FDgss++G++ i+ sD++l pdp 
  lcl|NCBI__GCF_000020385.1:WP_012469935.1   5 QVVEFAKENGALMVDYKFMDFVGTWQHVSVPITEFDEDTFEEGQGFDGSSIRGWQPIHASDMILLPDPT 73 
                                               78999**************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               +++++Pf a ++l++ic++++p+tke y rdpR+ia++ae +lk t++gd+++fGpEaEFf+fd+v+ +
  lcl|NCBI__GCF_000020385.1:WP_012469935.1  74 SAKMDPFVAVPTLSLICNIFDPITKEDYTRDPRNIARKAEAYLKsTGIGDTAFFGPEAEFFIFDEVRYD 142
                                               ********************************************************************* PP

                                 TIGR00653 139 easnssflevdseegewn.reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHH 206
                                               +++n++f+ vds+eg+wn  ++e  n gyk+++k+gYf+  pvD+++d+r+e+v++l+++g++ve +HH
  lcl|NCBI__GCF_000020385.1:WP_012469935.1 143 STANQAFYMVDSVEGAWNtGREEFPNLGYKPRHKEGYFPCSPVDSQNDLRNEMVMELQKVGIRVECQHH 211
                                               ******************5455566******************************************** PP

                                 TIGR00653 207 Evata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               Evat+ qaEid++f++lv++aD+++ +Kyv+knva ++Gkt+tFmpKpl+gdngsGmH+h+s+wkdg+n
  lcl|NCBI__GCF_000020385.1:WP_012469935.1 212 EVATGgQAEIDMRFSSLVDMADQLQWFKYVIKNVAYRNGKTVTFMPKPLYGDNGSGMHCHQSIWKDGQN 280
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                               lfag++ y gLs++al+yigGi+kHakal A+tnpt+nsYkRLvpG+EAPv++ays +nRsa++RiP++
  lcl|NCBI__GCF_000020385.1:WP_012469935.1 281 LFAGDK-YGGLSQMALWYIGGIIKHAKALCAITNPTTNSYKRLVPGFEAPVNMAYSSRNRSASLRIPMM 348
                                               ******.*************************************************************9 PP

                                 TIGR00653 344 a.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411
                                               + npkakR+E+R+pDps+n YLafaa+lmAgldGi+nkidpg+pldk++y ls+eelk+  i++ p sL
  lcl|NCBI__GCF_000020385.1:WP_012469935.1 349 StNPKAKRVEYRTPDPSCNGYLAFAAMLMAGLDGIENKIDPGQPLDKDIYGLSPEELKD--IPSAPGSL 415
                                               99*********************************************************..******** PP

                                 TIGR00653 412 eealdelesdk..evlkevlgeelieafielkr.kEveelrlkvhpvElekyld 462
                                               +eal+ le+d+  +++++v++ ++ie++ie+k+ +Ev+++r+++ p+E++ y+d
  lcl|NCBI__GCF_000020385.1:WP_012469935.1 416 DEALKCLEADHefLLKGDVFTPDVIEKWIEYKMeAEVNPVRMRPVPLEFALYYD 469
                                               ***********98899****************999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (470 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: 10.84
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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