Alignments for a candidate for glnA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Azospirillum brasilense Sp245

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate AZOBR_RS07095 AZOBR_RS07095 glutamine synthetase

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__azobra:AZOBR_RS07095
          Length = 469

 Score =  608 bits (1567), Expect = e-178
 Identities = 296/467 (63%), Positives = 359/467 (76%), Gaps = 2/467 (0%)

Query: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60
           +SK   LIK+HDVK++DLRFTD +G  HH        +++D FE G MFDGSSIAGWK I
Sbjct: 4   ISKVFDLIKEHDVKYVDLRFTDPRGKLHHTAQHV-STIDEDVFEDGIMFDGSSIAGWKAI 62

Query: 61  EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120
             SDMIL  D  TAV+DPF+   TL ++CD+ EPST Q Y R PR IA  AE+Y+ + GI
Sbjct: 63  NESDMILQLDPTTAVMDPFSAQPTLNILCDVYEPSTGQPYARCPRGIAKAAEKYMASAGI 122

Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180
           GDT + GPE EFF+FD+VKFK +++   ++  SE+G + SD+D E GN GHRPGVKGGYF
Sbjct: 123 GDTAYFGPEAEFFVFDDVKFKVEMNKVSYEFDSEEGPYTSDKDYEDGNLGHRPGVKGGYF 182

Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240
           PV P D   ++R  M + L EMG  VE HHHEVA A Q+E+G+KF+TLV+  D +Q  KY
Sbjct: 183 PVAPVDSGSDLRAEMLSVLAEMGVPVEKHHHEVA-ASQHELGIKFDTLVRTGDNMQYYKY 241

Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300
           VVHNVA AYG+TATFMPKP++GDNGSGMH+H SI K+G+  FAG  YA LSE ALY+IGG
Sbjct: 242 VVHNVAHAYGKTATFMPKPVFGDNGSGMHMHQSIWKEGQPLFAGNQYADLSELALYYIGG 301

Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360
           IIKH KALN FTNP TNSYKRLVPG+EAPV+LAYSARNRSAS RIPYV SP+G+R+E RF
Sbjct: 302 IIKHAKALNAFTNPTTNSYKRLVPGYEAPVLLAYSARNRSASCRIPYVASPKGKRVEVRF 361

Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420
           PDP+ANPYLAFAALLMAGLDGIQNKIHPG+A DKNLYDLP EE  ++P VCGSL+EAL+ 
Sbjct: 362 PDPSANPYLAFAALLMAGLDGIQNKIHPGEAMDKNLYDLPAEELAKVPTVCGSLREALDS 421

Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467
           L    AFL KG VF+ D I++YI L++EE +   T  HP+EY++YYS
Sbjct: 422 LKADSAFLQKGDVFTKDMIESYIDLRTEELLAFETMPHPIEYKMYYS 468


Lambda     K      H
   0.318    0.137    0.409 

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: 762
Number of extensions: 28
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: 468
Length of database: 469
Length adjustment: 33
Effective length of query: 435
Effective length of database: 436
Effective search space:   189660
Effective search space used:   189660
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 AZOBR_RS07095 AZOBR_RS07095 (glutamine synthetase)
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.20167.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-208  679.1   0.0   1.6e-208  679.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS07095  AZOBR_RS07095 glutamine syntheta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS07095  AZOBR_RS07095 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.0   0.0  1.6e-208  1.6e-208       2     462 .]       6     468 ..       5     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 679.0 bits;  conditional E-value: 1.6e-208
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +v++l+ke++vk+vdlrf+D +Gkl++ +  vs+++e+++e+gi+FDgss+ G+k+i+esD++l+ dp 
  lcl|FitnessBrowser__azobra:AZOBR_RS07095   6 KVFDLIKEHDVKYVDLRFTDPRGKLHHTAQHVSTIDEDVFEDGIMFDGSSIAGWKAINESDMILQLDPT 74 
                                               6899***************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t+v++Pf+a+++l++ cdvyep t++py r+pR iak ae+++  +++gd++yfGpEaEFf+fd+v+fk
  lcl|FitnessBrowser__azobra:AZOBR_RS07095  75 TAVMDPFSAQPTLNILCDVYEPSTGQPYARCPRGIAKAAEKYMAsAGIGDTAYFGPEAEFFVFDDVKFK 143
                                               ********************************************99*********************** PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                                ++n+  +e dseeg +   +++e gn g+++  kggYf+v+pvD+  d+r e++++l+e+g+ ve++H
  lcl|FitnessBrowser__azobra:AZOBR_RS07095 144 VEMNKVSYEFDSEEGPYTsdKDYEDGNLGHRPGVKGGYFPVAPVDSGSDLRAEMLSVLAEMGVPVEKHH 212
                                               ****************988899*********************************************** PP

                                 TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               HEva +q+E++ikfd+lv+++D+++ yKyvv+nva+ +GktatFmpKp+fgdngsGmH+h+s+wk+g++
  lcl|FitnessBrowser__azobra:AZOBR_RS07095 213 HEVAASQHELGIKFDTLVRTGDNMQYYKYVVHNVAHAYGKTATFMPKPVFGDNGSGMHMHQSIWKEGQP 281
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                               lfag++ ya+Lse alyyigGi+kHakal+A+tnpt+nsYkRLvpGyEAPv laysa+nRsa+ RiP++
  lcl|FitnessBrowser__azobra:AZOBR_RS07095 282 LFAGNQ-YADLSELALYYIGGIIKHAKALNAFTNPTTNSYKRLVPGYEAPVLLAYSARNRSASCRIPYV 349
                                               ******.************************************************************** PP

                                 TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412
                                               a+pk+kR+EvR+pDpsanpYLafaallmAgldGi+nki+pge++dknly+l+ eel++  ++++  sL+
  lcl|FitnessBrowser__azobra:AZOBR_RS07095 350 ASPKGKRVEVRFPDPSANPYLAFAALLMAGLDGIQNKIHPGEAMDKNLYDLPAEELAK--VPTVCGSLR 416
                                               **********************************************************..********* PP

                                 TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               eald+l++d+  + +++v+++++ie++i+l+++E   +++ +hp+E ++y++
  lcl|FitnessBrowser__azobra:AZOBR_RS07095 417 EALDSLKADSafLQKGDVFTKDMIESYIDLRTEELLAFETMPHPIEYKMYYS 468
                                               *********98889999*********************************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: 10.77
//
[ok]

This GapMind analysis is from Apr 09 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