Alignments for a candidate for glnA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Herbaspirillum seropedicae SmR1

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate HSERO_RS15690 HSERO_RS15690 glutamine synthetase

Query= BRENDA::P0A1P6
         (469 letters)



>FitnessBrowser__HerbieS:HSERO_RS15690
          Length = 471

 Score =  661 bits (1705), Expect = 0.0
 Identities = 314/468 (67%), Positives = 377/468 (80%)

Query: 2   SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61
           +A  VL M+ ++EVKFVD RF DT+GKEQHV++P    + + FE G  FDGSSI GWKGI
Sbjct: 4   TAAEVLKMVKDNEVKFVDFRFADTRGKEQHVSVPVSHFDIDKFESGHAFDGSSIAGWKGI 63

Query: 62  NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGI 121
             SDM+L+PD +TA IDPF  ++TL ++CD++EP   +GYDRDPRSIAKRAE YL+++G+
Sbjct: 64  EASDMLLIPDPNTANIDPFMEETTLFMQCDVIEPSDGKGYDRDPRSIAKRAEAYLKSSGL 123

Query: 122 ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYF 181
            DT  FGPEPEFF+FD +R+GA +SGS V ID  E +W++  K EGGN GHRP VKGGYF
Sbjct: 124 GDTAYFGPEPEFFIFDGVRWGADMSGSFVKIDSEEASWSTGAKIEGGNSGHRPTVKGGYF 183

Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241
           PVPPVDS QD+RSEM L++E +G+ VE HHHEVA AGQNE+ T+F+T+ ++AD  Q  KY
Sbjct: 184 PVPPVDSFQDMRSEMSLIIESLGIPVEVHHHEVAGAGQNELGTKFSTLVERADWTQTMKY 243

Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGG 301
           V+ NVAH +GKTATFMPKP+ GDNGSGMH H S+ K+G NLF+GD YAGLSE ALYYIGG
Sbjct: 244 VIWNVAHTYGKTATFMPKPLVGDNGSGMHVHQSVWKDGKNLFAGDGYAGLSEFALYYIGG 303

Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRF 361
           +IKHAKA+NA+ NP TNSYKRLVPG+EAPV LAYSARNRSASIRIP VA+PK RRIE RF
Sbjct: 304 IIKHAKALNAITNPGTNSYKRLVPGFEAPVKLAYSARNRSASIRIPHVANPKGRRIETRF 363

Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNA 421
           PDP ANPYLCF+ALLMAGLDG++NKIHPGEA  K+LY LPPEE K IP V  SL+EAL  
Sbjct: 364 PDPLANPYLCFSALLMAGLDGVQNKIHPGEAATKDLYHLPPEEDKLIPTVCSSLDEALEH 423

Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           LD DREFL  GGVFTD  IDAYI L+ +E  R RMT HP+EF++YYS+
Sbjct: 424 LDKDREFLTRGGVFTDSMIDAYIDLKMQEVQRFRMTTHPIEFDMYYSL 471


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: 747
Number of extensions: 22
Number of successful extensions: 1
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: 471
Length adjustment: 33
Effective length of query: 436
Effective length of database: 438
Effective search space:   190968
Effective search space used:   190968
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 HSERO_RS15690 HSERO_RS15690 (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.14222.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   9.6e-206  669.8   0.0   1.1e-205  669.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15690  HSERO_RS15690 glutamine syntheta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15690  HSERO_RS15690 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  669.6   0.0  1.1e-205  1.1e-205       2     462 .]       7     470 ..       6     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 669.6 bits;  conditional E-value: 1.1e-205
                                  TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdp 69 
                                                evlk++k+++vkfvd+rf+D++Gk+++v++pvs+++ + +e+g aFDgss+ G+k+ie sD+ll pdp
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690   7 EVLKMVKDNEVKFVDFRFADTRGKEQHVSVPVSHFDIDKFESGHAFDGSSIAGWKGIEASDMLLIPDP 74 
                                                6899**************************************************************** PP

                                  TIGR00653  70 etlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkve 136
                                                +t+ i+Pf++e++l + cdv ep +++ y+rdpRsiakrae +lk ++lgd++yfGpE+EFf+fd v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690  75 NTANIDPFMEETTLFMQCDVIEPSDGKGYDRDPRSIAKRAEAYLKsSGLGDTAYFGPEPEFFIFDGVR 142
                                                *********************************************99********************* PP

                                  TIGR00653 137 fkeasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelgleve 202
                                                 +  ++ sf+++dsee++w+  +++e+gn+g++++ kggYf+v+pvD+ +d+r+e+ l++e+lg+ ve
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690 143 WGADMSGSFVKIDSEEASWStgAKIEGGNSGHRPTVKGGYFPVPPVDSFQDMRSEMSLIIESLGIPVE 210
                                                *******************999999******************************************* PP

                                  TIGR00653 203 vsHHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslw 269
                                                v+HHEva a q+E+++kf++lv+ aD ++++Kyv+ nva+ +GktatFmpKpl+gdngsGmHvh+s+w
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690 211 VHHHEVAGAgQNELGTKFSTLVERADWTQTMKYVIWNVAHTYGKTATFMPKPLVGDNGSGMHVHQSVW 278
                                                *******999********************************************************** PP

                                  TIGR00653 270 kdgenlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsal 337
                                                kdg+nlfag+  yagLse alyyigGi+kHakal+A+tnp +nsYkRLvpG+EAPv+laysa+nRsa+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690 279 KDGKNLFAGDG-YAGLSEFALYYIGGIIKHAKALNAITNPGTNSYKRLVPGFEAPVKLAYSARNRSAS 345
                                                **********9.******************************************************** PP

                                  TIGR00653 338 iRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGie 405
                                                iRiP +anpk++RiE R+pDp anpYL+f+allmAgldG++nki+pge+  k+ly+l++ee k   i+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690 346 IRIPHVANPKGRRIETRFPDPLANPYLCFSALLMAGLDGVQNKIHPGEAATKDLYHLPPEEDKL--IP 411
                                                *************************************************************999..** PP

                                  TIGR00653 406 qlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                                ++ +sL+eal++l++d+  ++ ++v+++ +i+a+i+lk++Ev+++r++ hp+E+ +y++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15690 412 TVCSSLDEALEHLDKDRefLTRGGVFTDSMIDAYIDLKMQEVQRFRMTTHPIEFDMYYS 470
                                                *****************888999**********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (471 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.45
//
[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