Alignments for a candidate for glnA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Marinobacter adhaerens HP15

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate GFF440 HP15_428 glutamine synthetase, type I

Query= SwissProt::Q3V5W6
         (468 letters)



>FitnessBrowser__Marino:GFF440
          Length = 467

 Score =  692 bits (1786), Expect = 0.0
 Identities = 326/468 (69%), Positives = 389/468 (83%), Gaps = 1/468 (0%)

Query: 1   MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60
           MSK+V LIK+H+VKW+DLRFTD++G + HVT+PA + +++DFF  GKMFDGSSIAGWKGI
Sbjct: 1   MSKTVDLIKEHEVKWVDLRFTDSRGKEQHVTLPATE-VDEDFFADGKMFDGSSIAGWKGI 59

Query: 61  EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120
             SDMIL+PDD+T+VLDPFTE+ T+ + C+I+EPSTMQGY+RDPR++A RAEEYLK+TGI
Sbjct: 60  NESDMILMPDDETSVLDPFTEETTVNITCNIVEPSTMQGYERDPRSVARRAEEYLKSTGI 119

Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180
            D    GPEPEFF+FD VK+  D+ G+M+ I+SE+ +W+S +D +  N GHRPGVKGGYF
Sbjct: 120 ADGALFGPEPEFFVFDSVKWNVDMQGAMYHIHSEEAAWVSGEDFDRNNIGHRPGVKGGYF 179

Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240
           PVPP D  H++R AMC A+E MG  +EVHHHEV TAGQ EIGV  NTL KKADEVQ LKY
Sbjct: 180 PVPPVDSLHDLRGAMCAAMESMGLDIEVHHHEVGTAGQCEIGVGANTLTKKADEVQILKY 239

Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300
            VHNVA AYG+TATFMPKP+ GDNGSGMHVHMS++KDGKN FAG+ YAGLSE ALY+IGG
Sbjct: 240 CVHNVAHAYGKTATFMPKPVVGDNGSGMHVHMSLSKDGKNLFAGDSYAGLSEAALYYIGG 299

Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360
           +IKH KA+N FTN +TNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSP+ RRIE RF
Sbjct: 300 VIKHAKAINAFTNSSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPKARRIEVRF 359

Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420
           PDP+ANPYLAFAAL+MAGLDGIQNKIHPGDA DK+LYDLP EEA  IP V  +L EAL+ 
Sbjct: 360 PDPSANPYLAFAALMMAGLDGIQNKIHPGDAMDKDLYDLPKEEALSIPTVAETLSEALDC 419

Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468
           L+    FLT+GGVF++D I  Y+ LK  E  K+    HP+E++LYYSC
Sbjct: 420 LEADHEFLTRGGVFTEDMIAGYVGLKRGEVEKLNMTTHPIEFDLYYSC 467


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: 753
Number of extensions: 23
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: 468
Length of database: 467
Length adjustment: 33
Effective length of query: 435
Effective length of database: 434
Effective search space:   188790
Effective search space used:   188790
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 GFF440 HP15_428 (glutamine synthetase, type I)
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.4578.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-204  666.0   0.0   1.5e-204  665.8   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF440  HP15_428 glutamine synthetase, t


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF440  HP15_428 glutamine synthetase, type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.8   0.0  1.5e-204  1.5e-204       3     462 .]       4     466 ..       2     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 665.8 bits;  conditional E-value: 1.5e-204
                          TIGR00653   3 vlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPfr 78 
                                         ++l+ke++vk vdlrf+D +Gk+++v++p++e++e+++ +g++FDgss+ G+k+i+esD++l+pd et v +Pf+
  lcl|FitnessBrowser__Marino:GFF440   4 TVDLIKEHEVKWVDLRFTDSRGKEQHVTLPATEVDEDFFADGKMFDGSSIAGWKGINESDMILMPDDETSVLDPFT 79 
                                        56899*********************************************************************** PP

                          TIGR00653  79 aekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseeg 153
                                        +e++++++c++ ep t++ yerdpRs+a+raee+lk t+++d + fGpE+EFf+fd+v+ +  ++ ++++++see+
  lcl|FitnessBrowser__Marino:GFF440  80 EETTVNITCNIVEPSTMQGYERDPRSVARRAEEYLKsTGIADGALFGPEPEFFVFDSVKWNVDMQGAMYHIHSEEA 155
                                        **************************************************************************** PP

                          TIGR00653 154 ewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaa 226
                                        +w   ++++ +n g+++  kggYf+v+pvD+++d+r  ++ a+e++gl++ev+HHEv+ta q Ei++  ++l+k+a
  lcl|FitnessBrowser__Marino:GFF440 156 AWVsgEDFDRNNIGHRPGVKGGYFPVPPVDSLHDLRGAMCAAMESMGLDIEVHHHEVGTAgQCEIGVGANTLTKKA 231
                                        **977888999***************************************************************** PP

                          TIGR00653 227 DeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHaka 302
                                        De++++Ky v+nva+ +GktatFmpKp++gdngsGmHvh+sl+kdg+nlfag++ yagLse alyyigG++kHaka
  lcl|FitnessBrowser__Marino:GFF440 232 DEVQILKYCVHNVAHAYGKTATFMPKPVVGDNGSGMHVHMSLSKDGKNLFAGDS-YAGLSEAALYYIGGVIKHAKA 306
                                        ******************************************************.********************* PP

                          TIGR00653 303 laAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGik 378
                                        ++A+tn+++nsYkRLvpG+EAPv+laysa+nRsa+iRiP++ +pka+RiEvR+pDpsanpYLafaal+mAgldGi+
  lcl|FitnessBrowser__Marino:GFF440 307 INAFTNSSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPKARRIEVRFPDPSANPYLAFAALMMAGLDGIQ 382
                                        **************************************************************************** PP

                          TIGR00653 379 nkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkv 452
                                        nki+pg+++dk+ly+l++ee+ +  i++++e+L+eald le+d+  ++ ++v++e++i  ++ lkr Eve+l+++ 
  lcl|FitnessBrowser__Marino:GFF440 383 NKIHPGDAMDKDLYDLPKEEALS--IPTVAETLSEALDCLEADHefLTRGGVFTEDMIAGYVGLKRGEVEKLNMTT 456
                                        *********************99..*******************888999************************** PP

                          TIGR00653 453 hpvElekyld 462
                                        hp+E+  y++
  lcl|FitnessBrowser__Marino:GFF440 457 HPIEFDLYYS 466
                                        ********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (467 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: 10.07
//
[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