Alignments for a candidate for glnA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Klebsiella michiganensis M5al

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate BWI76_RS00400 BWI76_RS00400 glutamine synthetase

Query= BRENDA::P0A1P6
         (469 letters)



>FitnessBrowser__Koxy:BWI76_RS00400
          Length = 469

 Score =  914 bits (2361), Expect = 0.0
 Identities = 444/469 (94%), Positives = 461/469 (98%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIP+HQVNAEFFEEGKMFDGSSIGGWKG
Sbjct: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPSHQVNAEFFEEGKMFDGSSIGGWKG 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120
           INESDMVLMPDA+TA+IDPF+ + TLIIRCDILEPGTLQGYDRDPRSIAKRAE+YLR+TG
Sbjct: 61  INESDMVLMPDATTALIDPFYEEPTLIIRCDILEPGTLQGYDRDPRSIAKRAEEYLRSTG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180
           +ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY
Sbjct: 121 LADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPVPPVDS+QDIRS MC++ME+MGLVVEAHHHEVATAGQNE+ATRFNTMTKKADEIQIYK
Sbjct: 181 FPVPPVDSSQDIRSTMCMIMEEMGLVVEAHHHEVATAGQNEIATRFNTMTKKADEIQIYK 240

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300
           YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSL+KNG NLFSGDKYAGLSEQALYYIG
Sbjct: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFSGDKYAGLSEQALYYIG 300

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVR 360
           GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVV SPKARRIEVR
Sbjct: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVTSPKARRIEVR 360

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN
Sbjct: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420

Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           ALD DREFL AGGVFT++AIDAYIALR EE+DRVRMTPHPVEFELYYSV
Sbjct: 421 ALDADREFLTAGGVFTNDAIDAYIALRIEENDRVRMTPHPVEFELYYSV 469


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: 912
Number of extensions: 25
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: 469
Length adjustment: 33
Effective length of query: 436
Effective length of database: 436
Effective search space:   190096
Effective search space used:   190096
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 BWI76_RS00400 BWI76_RS00400 (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.7504.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.5e-222  723.1   0.0   7.3e-222  722.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00400  BWI76_RS00400 glutamine syntheta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00400  BWI76_RS00400 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.9   0.0  7.3e-222  7.3e-222       1     462 []       4     468 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 722.9 bits;  conditional E-value: 7.3e-222
                               TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpet 71 
                                             e+vl++l+e++vkfvdlrf+D+kGk+++v+ip +++++e++eeg++FDgss+ G+k+i+esD++l+pd+ t
  lcl|FitnessBrowser__Koxy:BWI76_RS00400   4 EHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPSHQVNAEFFEEGKMFDGSSIGGWKGINESDMVLMPDATT 74 
                                             578999***************************************************************** PP

                               TIGR00653  72 lvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeas 141
                                             + i+Pf +e++l+++cd+ ep t + y+rdpRsiakraee+l+ t+l+d+v fGpE+EFflfd+++f+ + 
  lcl|FitnessBrowser__Koxy:BWI76_RS00400  75 ALIDPFYEEPTLIIRCDILEPGTLQGYDRDPRSIAKRAEEYLRsTGLADTVLFGPEPEFFLFDDIRFGASI 145
                                             *********************************************************************** PP

                               TIGR00653 142 nssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvat 210
                                             + s++++d++eg+wn  +++e+gnkg+++  kggYf+v+pvD+ +dir+ +++++ee+gl ve++HHEvat
  lcl|FitnessBrowser__Koxy:BWI76_RS00400 146 SGSHVAIDDIEGAWNssTKYEGGNKGHRPGVKGGYFPVPPVDSSQDIRSTMCMIMEEMGLVVEAHHHEVAT 216
                                             ***************99999*************************************************** PP

                               TIGR00653 211 a.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfagee 280
                                             a q+Ei+++f++++k+aDei++yKyvv+nva++ GktatFmpKp+fgdngsGmH+h+sl+k+g nlf+g++
  lcl|FitnessBrowser__Koxy:BWI76_RS00400 217 AgQNEIATRFNTMTKKADEIQIYKYVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFSGDK 287
                                             *********************************************************************** PP

                               TIGR00653 281 gyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRi 351
                                              yagLse+alyyigG++kHaka++Al+npt+nsYkRLvpGyEAPv+laysa+nRsa+iRiP++++pka+Ri
  lcl|FitnessBrowser__Koxy:BWI76_RS00400 288 -YAGLSEQALYYIGGVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVTSPKARRI 357
                                             .********************************************************************** PP

                               TIGR00653 352 EvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk 422
                                             EvR+pDp+anpYL+faallmAgldGiknki+pge++dknly+l++ee+ke  i+q++ sLeeal++l++d+
  lcl|FitnessBrowser__Koxy:BWI76_RS00400 358 EVRFPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKE--IPQVAGSLEEALNALDADR 426
                                             **************************************************..******************* PP

                               TIGR00653 423 ..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               +++++v+++++i+a+i+l+ +E +++r+++hpvE+e y++
  lcl|FitnessBrowser__Koxy:BWI76_RS00400 427 efLTAGGVFTNDAIDAYIALRIEENDRVRMTPHPVEFELYYS 468
                                             88999***********************************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: 7.52
//
[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