Alignments for a candidate for glnA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Phaeobacter inhibens BS107

Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate GFF1845 PGA1_c18720 glutamine synthetase GlnA

Query= CharProtDB::CH_024014
         (469 letters)



>FitnessBrowser__Phaeo:GFF1845
          Length = 468

 Score =  606 bits (1563), Expect = e-178
 Identities = 285/468 (60%), Positives = 361/468 (77%), Gaps = 1/468 (0%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MSA+ VL M+ + ++ +VD+RFTD +GK QHVT+    V+ +F EEG MFDGSSI GWK 
Sbjct: 1   MSADAVLKMIKDEDIAYVDIRFTDVRGKLQHVTVDVDLVDEDFIEEGFMFDGSSIAGWKS 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120
           I  SDM L+ D S+A IDPF+A+ TL I C ++EP T + Y RDPR  A++AE YL+S+G
Sbjct: 61  IENSDMKLILDTSSAYIDPFYAEKTLCIHCSVVEPDTGEAYPRDPRGTAQKAEAYLKSSG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180
           I D    GPE EFFLFDD+RF ++I+     +D  + +WN+ T+YE GN GHRP +KGGY
Sbjct: 121 IGDVAYMGPEAEFFLFDDVRFSNTINKVSFEVDATDASWNTDTEYEMGNMGHRPGIKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPV P+D AQD+RSEM   M+++G+ V+ HHHEVA+  Q+E+   F+++TK+ADE+Q YK
Sbjct: 181 FPVNPIDEAQDLRSEMLSTMKRLGMKVDKHHHEVASC-QHELGLIFDSLTKQADELQKYK 239

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300
           YV+HNVAH +GK+ATFMPKP++GDNG+GMH +MS+ K+G  LFAGDKYA LS +ALY+IG
Sbjct: 240 YVIHNVAHAYGKSATFMPKPIYGDNGTGMHVNMSIWKDGKPLFAGDKYADLSNEALYFIG 299

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360
           G++KHAK +NA  NP+TNSYKRL+PG+EAPV+ AYSARNRS  +RIP   SPKA+R+E R
Sbjct: 300 GILKHAKTLNAFTNPSTNSYKRLIPGFEAPVLRAYSARNRSGCVRIPWTESPKAKRVEAR 359

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDPAANPYLCFAALLMAGLDGIKNKI PGEAMDKNLYDLP EE  +IP V GSL EAL 
Sbjct: 360 FPDPAANPYLCFAALLMAGLDGIKNKIDPGEAMDKNLYDLPAEELADIPTVCGSLREALE 419

Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468
            L  D +FL  G VFT + I+ YIAL+ EE +    TPHPVE+ +YYS
Sbjct: 420 SLAGDHDFLLQGDVFTKDQIEGYIALKMEEVETYEHTPHPVEYGMYYS 467


Lambda     K      H
   0.318    0.136    0.400 

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: 675
Number of extensions: 19
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: 469
Length of database: 468
Length adjustment: 33
Effective length of query: 436
Effective length of database: 435
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 GFF1845 PGA1_c18720 (glutamine synthetase GlnA)
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.16997.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-200  652.4   0.0     2e-200  652.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1845  PGA1_c18720 glutamine synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1845  PGA1_c18720 glutamine synthetase GlnA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  652.3   0.0    2e-200    2e-200       2     462 .]       5     467 ..       4     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 652.3 bits;  conditional E-value: 2e-200
                          TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPf 77 
                                         vlk++k+e++ +vd+rf+D++Gkl++v++ v+ ++e+++eeg +FDgss+ G+ksie+sD+ l  d++++ i+Pf
  lcl|FitnessBrowser__Phaeo:GFF1845   5 AVLKMIKDEDIAYVDIRFTDVRGKLQHVTVDVDLVDEDFIEEGFMFDGSSIAGWKSIENSDMKLILDTSSAYIDPF 80 
                                        5899************************************************************************ PP

                          TIGR00653  78 raekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdsee 152
                                         aek+l + c+v ep t+e y rdpR +a++ae +lk +++gd +y+GpEaEFflfd+v+f+++ n+  +evd+++
  lcl|FitnessBrowser__Phaeo:GFF1845  81 YAEKTLCIHCSVVEPDTGEAYPRDPRGTAQKAEAYLKsSGIGDVAYMGPEAEFFLFDDVRFSNTINKVSFEVDATD 156
                                        *************************************99************************************* PP

                          TIGR00653 153 gewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidikfdklvkaa 226
                                        ++wn  +e+e gn g+++  kggYf+v+p+D+a+d+r+e+++++++lg++v+++HHEva+ q+E+++ fd+l+k+a
  lcl|FitnessBrowser__Phaeo:GFF1845 157 ASWNtdTEYEMGNMGHRPGIKGGYFPVNPIDEAQDLRSEMLSTMKRLGMKVDKHHHEVASCQHELGLIFDSLTKQA 232
                                        ****88899999**************************************************************** PP

                          TIGR00653 227 DeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHaka 302
                                        De+++yKyv++nva+ +Gk atFmpKp++gdng GmHv++s+wkdg++lfag++ ya+Ls++aly+igGilkHak+
  lcl|FitnessBrowser__Phaeo:GFF1845 233 DELQKYKYVIHNVAHAYGKSATFMPKPIYGDNGTGMHVNMSIWKDGKPLFAGDK-YADLSNEALYFIGGILKHAKT 307
                                        ******************************************************.********************* PP

                          TIGR00653 303 laAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGik 378
                                        l+A+tnp++nsYkRL+pG+EAPv  aysa+nRs ++RiP + +pkakR+E R+pDp+anpYL+faallmAgldGik
  lcl|FitnessBrowser__Phaeo:GFF1845 308 LNAFTNPSTNSYKRLIPGFEAPVLRAYSARNRSGCVRIPWTESPKAKRVEARFPDPAANPYLCFAALLMAGLDGIK 383
                                        **************************************************************************** PP

                          TIGR00653 379 nkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkv 452
                                        nkidpge++dknly+l+ eel++  i+++  sL+eal++l+ d+  +++++v++++ ie +i+lk++Eve+++ ++
  lcl|FitnessBrowser__Phaeo:GFF1845 384 NKIDPGEAMDKNLYDLPAEELAD--IPTVCGSLREALESLAGDHdfLLQGDVFTKDQIEGYIALKMEEVETYEHTP 457
                                        ***********************..******************988999*************************** PP

                          TIGR00653 453 hpvElekyld 462
                                        hpvE  +y++
  lcl|FitnessBrowser__Phaeo:GFF1845 458 HPVEYGMYYS 467
                                        ********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (468 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: 9.45
//
[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