Alignments for a candidate for asnB in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Bradyrhizobium sp. BTAi1

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_012043792.1 BBTA_RS17340 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000015165.1:WP_012043792.1
          Length = 647

 Score =  176 bits (445), Expect = 4e-48
 Identities = 155/583 (26%), Positives = 259/583 (44%), Gaps = 82/583 (14%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVW--GEHHVLFGHKRLAVVDIEG 58
           MCG+ G   +   +  ++  + R    L  RGPD + +W   +  V  GH RL+++D+  
Sbjct: 1   MCGLAGVWCWDTPI--DRPAIARALGLLDHRGPDGNGLWISEDGKVALGHTRLSIIDLVT 58

Query: 59  GRQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCV 118
           G QP++  +      ++ NGE Y+ E +R +L ARG +F   SD+E+ L  Y E    C 
Sbjct: 59  GEQPLS--HPNGKLQLVVNGEFYDYERIRNDLTARGARFRTRSDSEIALWLYDESGTRCF 116

Query: 119 DHLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVD 178
             LNG FAF +WD     L AARDR G+KP FY  +    L  SEIKA+LA   + A+ D
Sbjct: 117 ADLNGEFAFILWDAGAGRLIAARDRFGIKPLFYAVQSGRILLASEIKALLA-MGVPAQWD 175

Query: 179 RTGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWRYWNVESEKHTDSFDD- 237
             G  +   +  + T    +F GI+++ P   L+ ++ G+ I RYW+          +D 
Sbjct: 176 VEGYLDAAHVLQNGT----LFSGIRQVPPGCYLSATRHGITIQRYWDAPFASALSPIEDE 231

Query: 238 --TVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSID 295
              +  +R+    A   ++ +DVPV  +LSGG+DS ++ A+AA       +AP   ++I 
Sbjct: 232 HGALDQIRAQMSRATRWRMRADVPVAAYLSGGIDSMSVLALAAA---TTNRAP-DAFTIA 287

Query: 296 YEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMA 355
           YE+       +A+   D+    E      GT  H+  ++   L DH   ++   +     
Sbjct: 288 YED-------AAY---DESHRAESFATQLGTRFHRVPVNGAALADHFATSLWHSETACFN 337

Query: 356 DVDSSLLWFCREIK-KDFVVSLSGECADEIFGGYPWFHTADVESGFPWMR---------- 404
              ++     + ++   + V L+GE ADEIF GY      D   G   M+          
Sbjct: 338 PHGTAKFILSKAVRDAGYKVVLTGEGADEIFAGYA-PSRVDALGGSAAMQAMIATRDRAT 396

Query: 405 -------STEERIKLLSDSWQKKLNLKEYVNAKYEETLAETPLL--DGETGVDKARRQLF 455
                  +  +++ L++   Q+   +  ++  +    L    LL  D  T     R    
Sbjct: 397 YAVTPQHTATDQLPLIA---QRFGTVPTWLRHQMAHLLGVADLLRDDLRTAWSTDRPLAA 453

Query: 456 YLNML--WFMTNLLDRKDRMSMGASLEVRVPFADHRLV--------------------EY 493
           +L  L  W +  L    D + +G +L ++    ++ LV                      
Sbjct: 454 FLKYLEPWTVPAL----DTVDLGIALMLKTTLPNYVLVTLGDRMEMAHSIEGRLPFLDHQ 509

Query: 494 VWNIPW----EMKMHDNREKGILRKALEGILPDDILYRKKSPY 532
           V  + W     +K+ D  EK  LR+A+  +LP D + R+K P+
Sbjct: 510 VVELAWRLPSHLKIRDGVEKFALRQAMRNLLPADAVDRQKHPF 552


Lambda     K      H
   0.320    0.137    0.425 

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: 914
Number of extensions: 41
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 614
Length of database: 647
Length adjustment: 38
Effective length of query: 576
Effective length of database: 609
Effective search space:   350784
Effective search space used:   350784
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: 54 (25.4 bits)

Align candidate WP_012043792.1 BBTA_RS17340 (asparagine synthase (glutamine-hydrolyzing))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# 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/TIGR01536.hmm
# target sequence database:        /tmp/gapView.2237790.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-127  412.0   0.0   3.2e-127  411.6   0.0    1.2  1  NCBI__GCF_000015165.1:WP_012043792.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015165.1:WP_012043792.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.6   0.0  3.2e-127  3.2e-127       1     517 []       2     552 ..       2     552 .. 0.88

  Alignments for each domain:
  == domain 1  score: 411.6 bits;  conditional E-value: 3.2e-127
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cg+ag+   ++ +++   ai++ l +l hRGPD++g+w++ ++ +++lgh RL+iidl +g+QPls  + + +
  NCBI__GCF_000015165.1:WP_012043792.1   2 CGLAGVWCWDTPIDR--PAIARALGLLDHRGPDGNGLWIS-EDGKVALGHTRLSIIDLVTGEQPLSHPNgKLQ 71 
                                           999998877776555..799999*****************.799***********************999*** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +v+nGE Y +e +r++l ++G +F+t+sD+E+ L +y+e g +++++L+G+FAf+lwd+ +g+l++aRDr+Gi
  NCBI__GCF_000015165.1:WP_012043792.1  72 LVVNGEFYDYERIRNDLTARGARFRTRSDSEIALWLYDESGTRCFADLNGEFAFILWDAGAGRLIAARDRFGI 144
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPL+ya ++g++l aSEiKalla+  ++a+ d e++ +   +    ++ tlf ++++++p+ +l   ++  ++
  NCBI__GCF_000015165.1:WP_012043792.1 145 KPLFYAVQSGRILLASEIKALLAMG-VPAQWDVEGYLDAAHVL---QNGTLFSGIRQVPPGCYLsatRHGITI 213
                                           *************************.9*******999988877...589**************9888788899 PP

                             TIGR01536 216 eeywevekee...vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsi 285
                                           ++yw++   +     e+e+ + +++r  + +a++ r++advpv+++lSGG+DS +v a+a++  +++   F+i
  NCBI__GCF_000015165.1:WP_012043792.1 214 QRYWDAPFASalsPIEDEHGALDQIRAQMSRATRWRMRADVPVAAYLSGGIDSMSVLALAAATTNRAPDAFTI 286
                                           99****999888777889999********************************************99****** PP

                             TIGR01536 286 gfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVv 358
                                           ++e ++++des+ a+  a +lgt+ ++v ++ ++++++++  +++ e    ++  +  ++lsk++r+ g+kVv
  NCBI__GCF_000015165.1:WP_012043792.1 287 AYE-DAAYDESHRAESFATQLGTRFHRVPVNGAALADHFATSLWHSETACFNPHGTAKFILSKAVRDAGYKVV 358
                                           ***.9******************************************9999********************** PP

                             TIGR01536 359 LsGeGaDElfgGYeyfreakaeeale..........lpeaselaekkl......................... 396
                                           L+GeGaDE+f+GY+  r       +                      +                         
  NCBI__GCF_000015165.1:WP_012043792.1 359 LTGEGADEIFAGYAPSRVDALGGSAAmqamiatrdrA----------Tyavtpqhtatdqlpliaqrfgtvpt 421
                                           *************988776665555522333333330..........23334444555666766666677776 PP

                             TIGR01536 397 llqaklakeselkellkakleeelkekeelkkelkee........seleellrldlelllsdllrak..Drvs 459
                                            l++++a+    + ll+ +l+++ ++ + l++ lk           +++  + l l++ l++++++   Dr+ 
  NCBI__GCF_000015165.1:WP_012043792.1 422 WLRHQMAHLLGVADLLRDDLRTAWSTDRPLAAFLKYLepwtvpalDTVDLGIALMLKTTLPNYVLVTlgDRME 494
                                           444455555555555555555544444444444333356667677778888889999999999998888**** PP

                             TIGR01536 460 mahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           mahs+E R PflD+++vela+++p  lk+rdg eK+ Lr+a+++llP + ++R+K++f
  NCBI__GCF_000015165.1:WP_012043792.1 495 MAHSIEGRLPFLDHQVVELAWRLPSHLKIRDGVEKFALRQAMRNLLPADAVDRQKHPF 552
                                           *******************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (647 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: 00:00:00.01
# Mc/sec: 24.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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