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.3212.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.57
//
[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:

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:

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:

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:

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