Alignments for a candidate for glnA in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Paraburkholderia sp. CCGE1002

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_013089840.1 BC1002_RS09550 type I glutamate--ammonia ligase

Query= SwissProt::Q3V5W6
         (468 letters)



>NCBI__GCF_000092885.1:WP_013089840.1
          Length = 471

 Score =  654 bits (1688), Expect = 0.0
 Identities = 312/471 (66%), Positives = 380/471 (80%), Gaps = 5/471 (1%)

Query: 1   MSKSV----QLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAG 56
           MSKSV    QL+KD DVK++D RFTDT+G + HV++P   A ++D FE G  FDGSSIAG
Sbjct: 1   MSKSVADVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPV-SAFDEDKFESGHAFDGSSIAG 59

Query: 57  WKGIEASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLK 116
           WKGIEASDM+L+PD +TA +DPF E++TL+L CD++EP+  +GY+RDPR++A RAE YLK
Sbjct: 60  WKGIEASDMLLVPDANTAFIDPFFEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLK 119

Query: 117 TTGIGDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVK 176
           ++G+GDT F GPEPEFFIFD V++ +D SG   KI SE+  W S ++ EGGN GHRPG K
Sbjct: 120 SSGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFIKIGSEEAPWSSAKEFEGGNTGHRPGTK 179

Query: 177 GGYFPVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQ 236
           GGYFPV P D   +IR+ MC  LE++G  VEVHHHEVA  GQNEIG KF+TLV++AD +Q
Sbjct: 180 GGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHHHEVAGQGQNEIGTKFSTLVQRADWLQ 239

Query: 237 TLKYVVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALY 296
            +KY++HNVA  YG+TATFMPKP+ GDNGSGMHVH SI KDG+N FAG GYAGLSE AL+
Sbjct: 240 QMKYIIHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKDGQNLFAGNGYAGLSEFALF 299

Query: 297 FIGGIIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRI 356
           +IGGIIKH +ALN  TNP TNSYKRLVP FEAPV LAYSARNRSASIRIP+V++P+GRRI
Sbjct: 300 YIGGIIKHARALNAITNPGTNSYKRLVPHFEAPVKLAYSARNRSASIRIPHVSNPKGRRI 359

Query: 357 EARFPDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKE 416
           E RFPDP ANPYL F+AL+MAGLDG+QNKIHPG+AADKNLYDLPPEE  +IP VC  L +
Sbjct: 360 ETRFPDPLANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAKIPTVCAGLDQ 419

Query: 417 ALEELDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467
           AL+ LD  R FLT+GGVF+D  +DAYI LK+ E  + R  VHP+E+E+YYS
Sbjct: 420 ALDALDADREFLTRGGVFTDSMLDAYIELKTGELQRYRQSVHPIEFEMYYS 470


Lambda     K      H
   0.318    0.137    0.409 

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: 777
Number of extensions: 23
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: 468
Length of database: 471
Length adjustment: 33
Effective length of query: 435
Effective length of database: 438
Effective search space:   190530
Effective search space used:   190530
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 WP_013089840.1 BC1002_RS09550 (type I glutamate--ammonia ligase)
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.1111.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-204  663.5   0.0   8.6e-204  663.4   0.0    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013089840.1  BC1002_RS09550 type I glutamate-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013089840.1  BC1002_RS09550 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.4   0.0  8.6e-204  8.6e-204       2     462 .]       7     470 ..       6     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 663.4 bits;  conditional E-value: 8.6e-204
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +v++l+k+e+vkfvd+rf+D++Gk+++v++pvs+++e+ +e+g aFDgss+ G+k+ie sD+ll+pd++
  lcl|NCBI__GCF_000092885.1:WP_013089840.1   7 DVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPVSAFDEDKFESGHAFDGSSIAGWKGIEASDMLLVPDAN 75 
                                               68899**************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               t++i+Pf +e++l+++cdv ep++++ yerdpRs akrae +lk ++lgd+++fGpE+EFf+fd+v+ +
  lcl|NCBI__GCF_000092885.1:WP_013089840.1  76 TAFIDPFFEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLKsSGLGDTAFFGPEPEFFIFDSVQWN 144
                                               ********************************************99*********************** PP

                                 TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                               + ++  f+++ see+ w+  +e+e+gn+g+++ +kggYf+v+pvD+ +dir+e++l le++g+ vev+H
  lcl|NCBI__GCF_000092885.1:WP_013089840.1 145 TDQSGCFIKIGSEEAPWSsaKEFEGGNTGHRPGTKGGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHH 213
                                               *****************999999********************************************** PP

                                 TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273
                                               HEva   q+Ei++kf++lv+ aD ++++Ky+++nva+ +GktatFmpKp++gdngsGmHvh+s+wkdg+
  lcl|NCBI__GCF_000092885.1:WP_013089840.1 214 HEVAGQgQNEIGTKFSTLVQRADWLQQMKYIIHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKDGQ 282
                                               ***9666************************************************************** PP

                                 TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342
                                               nlfag+  yagLse al+yigGi+kHa+al+A+tnp +nsYkRLvp +EAPv+laysa+nRsa+iRiP 
  lcl|NCBI__GCF_000092885.1:WP_013089840.1 283 NLFAGNG-YAGLSEFALFYIGGIIKHARALNAITNPGTNSYKRLVPHFEAPVKLAYSARNRSASIRIPH 350
                                               ******9.************************************************************* PP

                                 TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411
                                               ++npk++RiE R+pDp anpYL+f+al+mAgldG++nki+pge+ dknly+l++ee ++  i+++ + L
  lcl|NCBI__GCF_000092885.1:WP_013089840.1 351 VSNPKGRRIETRFPDPLANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAK--IPTVCAGL 417
                                               ***********************************************************..******** PP

                                 TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               ++ald+l++d+  ++ ++v+++ +++a+ielk+ E +++r +vhp+E+e+y++
  lcl|NCBI__GCF_000092885.1:WP_013089840.1 418 DQALDALDADRefLTRGGVFTDSMLDAYIELKTGELQRYRQSVHPIEFEMYYS 470
                                               ***********888999**********************************96 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: 10.95
//
[ok]

This GapMind analysis is from Apr 10 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