Alignments for a candidate for glnA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Dinoroseobacter shibae DFL-12

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate 3608471 Dshi_1867 glutamine synthetase catalytic region (RefSeq)

Query= SwissProt::O87393
         (435 letters)



>FitnessBrowser__Dino:3608471
          Length = 438

 Score =  659 bits (1701), Expect = 0.0
 Identities = 319/439 (72%), Positives = 360/439 (82%), Gaps = 5/439 (1%)

Query: 1   MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60
           MT DL+ FA++ GVKYFMIS+TDLFGGQRAKLVPA AIA MQ  GAGFAGFATW D+TPA
Sbjct: 1   MTTDLAQFAKDTGVKYFMISFTDLFGGQRAKLVPAPAIAGMQAEGAGFAGFATWLDMTPA 60

Query: 61  HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120
           HPD+ A+PD ++VIQLPWK +VAWVAA+C+M+   V QAPR  L + V  AA +GL VKT
Sbjct: 61  HPDMLAVPDPASVIQLPWKPEVAWVAANCVMEGVSVAQAPRNTLIRQVEAAAAQGLHVKT 120

Query: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180
           GVE EFFL++ DGSKISD  DTAEKPCYDQ AIMRRYDVIAEI DYML LGW PYQ DHE
Sbjct: 121 GVEAEFFLLTADGSKISDPADTAEKPCYDQGAIMRRYDVIAEIGDYMLALGWGPYQADHE 180

Query: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240
           DANGQFEMNW++DDAL TADKHSFFKFMVKS+AEKHGLRATFMPKP   LTGNGCH HIS
Sbjct: 181 DANGQFEMNWDFDDALATADKHSFFKFMVKSVAEKHGLRATFMPKPMPELTGNGCHTHIS 240

Query: 241 VWDLAGEVNAFADN----KAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPR 296
           VWD  G  N FA        E GLS  GRHFLGG+M HA AL A+TNPTVNSYKR+NAP 
Sbjct: 241 VWDAEG-TNVFAGQGDGPTGEVGLSEAGRHFLGGLMHHARALTALTNPTVNSYKRLNAPT 299

Query: 297 TISGATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSK 356
           T SGATWAPN+VTWTGNNRTHMVRVPGPGRFELRLPDGA NPYLLQA IIAAGLSG+ ++
Sbjct: 300 TTSGATWAPNAVTWTGNNRTHMVRVPGPGRFELRLPDGAANPYLLQAAIIAAGLSGLATR 359

Query: 357 ADPGRHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGE 416
           ADPG  +DIDMY +GH +TD PKLPLNLLDALR ++ D  L+ ALG +F++A+LKLK+ E
Sbjct: 360 ADPGPRHDIDMYAEGHTLTDTPKLPLNLLDALRAFDADTTLKTALGPDFASAFLKLKRAE 419

Query: 417 WNTYCSQFTEWEHQTTLDV 435
           W+ Y S F+ WE + TLDV
Sbjct: 420 WDAYVSHFSRWEKEHTLDV 438


Lambda     K      H
   0.319    0.135    0.421 

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: 712
Number of extensions: 29
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: 435
Length of database: 438
Length adjustment: 32
Effective length of query: 403
Effective length of database: 406
Effective search space:   163618
Effective search space used:   163618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 3608471 Dshi_1867 (glutamine synthetase catalytic region (RefSeq))
to HMM TIGR03105 (glnT: glutamine synthetase, type III (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/TIGR03105.hmm
# target sequence database:        /tmp/gapView.23599.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03105  [M=435]
Accession:   TIGR03105
Description: gln_synth_III: glutamine synthetase, type III
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-201  656.0   0.0   1.2e-201  655.8   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608471  Dshi_1867 glutamine synthetase c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608471  Dshi_1867 glutamine synthetase catalytic region (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.8   0.0  1.2e-201  1.2e-201       2     435 .]       6     437 ..       5     437 .. 0.99

  Alignments for each domain:
  == domain 1  score: 655.8 bits;  conditional E-value: 1.2e-201
                         TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlPwkpe 78 
                                       +++++++gvky++++f+dl+G ++aklvP+ a++ +++egagfaGfa++ l+++Pa++d+lavpd++s+iqlPwkpe
  lcl|FitnessBrowser__Dino:3608471   6 AQFAKDTGVKYFMISFTDLFGGQRAKLVPAPAIAGMQAEGAGFAGFATW-LDMTPAHPDMLAVPDPASVIQLPWKPE 81 
                                       789**********************************************.*************************** PP

                         TIGR03105  79 vawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpcYDqralmr 155
                                       vawvaa++v+eg +v++apR+ l ++++ aa++g+++ktGve+effll+++   +++++D aD+++kpcYDq a+mr
  lcl|FitnessBrowser__Dino:3608471  82 VAWVAANCVMEGVSVAQAPRNTLIRQVEAAAAQGLHVKTGVEAEFFLLTAD---GSKISDPADTAEKPCYDQGAIMR 155
                                       *************************************************99...889******************** PP

                         TIGR03105 156 rydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeegllatfmPkPfadrtG 232
                                       rydv++ei +++ +lGw++Yq DheDanGqfe+n++++Dal taD+++ffk++vk++ae++gl+atfmPkP+ ++tG
  lcl|FitnessBrowser__Dino:3608471 156 RYDVIAEIGDYMLALGWGPYQADHEDANGQFEMNWDFDDALATADKHSFFKFMVKSVAEKHGLRATFMPKPMPELTG 232
                                       ***************************************************************************** PP

                         TIGR03105 233 nGlhlhlslldedgknlfaddad..eeglglsklayhfiaGilkhakaLaallaPtvnsYkRlvakrtlsgatWaPa 307
                                       nG+h+h+s++d++g+n+fa + d  + ++gls+ + hf++G+++ha+aL+al++PtvnsYkRl+a++t+sgatWaP+
  lcl|FitnessBrowser__Dino:3608471 233 NGCHTHISVWDAEGTNVFAGQGDgpTGEVGLSEAGRHFLGGLMHHARALTALTNPTVNSYKRLNAPTTTSGATWAPN 309
                                       ********************99987899************************************************* PP

                         TIGR03105 308 lisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkdenlyaeelaekgvetLPqt 384
                                        ++++gnnRthmvR+P++gR+elRl+DgaanpYl++aa++aaGL G++ ++dpg+r+d+++yae+++ +++ +LP +
  lcl|FitnessBrowser__Dino:3608471 310 AVTWTGNNRTHMVRVPGPGRFELRLPDGAANPYLLQAAIIAAGLSGLATRADPGPRHDIDMYAEGHTLTDTPKLPLN 386
                                       ***************************************************************************** PP

                         TIGR03105 385 LlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryle 435
                                       Ll+alra++ad+ l+ alG +++++flklkr ew++y +++s We +++l+
  lcl|FitnessBrowser__Dino:3608471 387 LLDALRAFDADTTLKTALGPDFASAFLKLKRAEWDAYVSHFSRWEKEHTLD 437
                                       ***********************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (438 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: 00:00:00.02
# Mc/sec: 6.75
//
[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