Alignments for a candidate for asnB in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Kyrpidia tusciae DSM 2912

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_013074357.1 BTUS_RS01465 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000092905.1:WP_013074357.1
          Length = 613

 Score =  637 bits (1642), Expect = 0.0
 Identities = 303/613 (49%), Positives = 397/613 (64%), Gaps = 3/613 (0%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDIEGGR 60
           MCGI GW+D+  ++ +++  +  M D    RGPD   +W        H+RL+++D EGG 
Sbjct: 1   MCGIAGWIDWNVEMTEQRPVLKAMADVQYWRGPDAEGIWMSRRAGLAHRRLSIIDPEGGA 60

Query: 61  QPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVDH 120
           QPM   +   T  I+YNGELYN  +L++EL   G+ F    DTEV+L +Y  W   CV+ 
Sbjct: 61  QPMIRRHGERTLVIVYNGELYNMAELQRELEGLGYTFATRCDTEVVLVAYAHWGPACVER 120

Query: 121 LNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDRT 180
            NGI+A  +WDE+   LF ARDRLGVKP FY    S  +F SE+K +LAHP ++  VD  
Sbjct: 121 FNGIYAIGIWDEQSQELFLARDRLGVKPLFYAPLASGLVFASELKGLLAHPAVRPEVDSE 180

Query: 181 GLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWRYWNVESEKHTDSFDDTVA 240
           GL+EIF +GP RTPG G+F+   E++P  AL F + GL+  +YW +ES  H D  + T+A
Sbjct: 181 GLAEIFAMGPGRTPGHGVFRNTCEVKPGWALLFDRRGLHHRQYWKLESRPHEDDLETTIA 240

Query: 241 NVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSIDYEEND 300
            VR L +D V RQL+SDVPVCT LSGGLDSSAITA AA  F ++G+ PL T+SIDY +ND
Sbjct: 241 TVRDLLEDTVGRQLMSDVPVCTLLSGGLDSSAITAFAARAFRRQGRPPLRTFSIDYVDND 300

Query: 301 KYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMADVDSS 360
            YFQ +AFQP  DGPW E++ +          ++   + D L EAV  +DLPGM D+DSS
Sbjct: 301 VYFQPNAFQPAADGPWAERVADFLQVDRRIVTLTPAAVADALREAVRARDLPGMTDIDSS 360

Query: 361 LLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVESG--FPWMRSTEERIKLLSDSWQ 418
           LL FCREIKK+  V+LSGECADE+FGGYPWFH  +      FPW     ERI +L   + 
Sbjct: 361 LLLFCREIKKEATVALSGECADEVFGGYPWFHRKEALEADVFPWSLKMRERISVLHPDFV 420

Query: 419 KKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMTNLLDRKDRMSMGAS 478
             +  ++YV  +Y E L   P L GE   D   R++FYLN+  +M  LLDRKDRMSM   
Sbjct: 421 DHVQPEQYVRRRYREVLDAVPRLTGENPQDARIREMFYLNLFHWMPVLLDRKDRMSMAVG 480

Query: 479 LEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDILYRKKSPYPKTHHP 538
           LEVRVPF DHRLVEY+WN+PW +KM   REKG+LR A++G+LPDD L+RKKSP+PKTHHP
Sbjct: 481 LEVRVPFCDHRLVEYMWNVPWSIKMAAGREKGLLRLAMKGLLPDDALWRKKSPFPKTHHP 540

Query: 539 EYTKGVSEWLKTIRSQKDSVLHTLLDRKQLDQLLETEGSSFKVPWFGQLMKGPQLIAHLA 598
           ++ +     L+ +     S L  L+D K + Q L+ EG  F +PWFGQLM+ PQL A+L 
Sbjct: 541 DFARACRSALQEVLVDSSSPLLPLIDVKSIHQWLQAEG-EFDIPWFGQLMRLPQLFAYLV 599

Query: 599 QIHTWFEAYRIDI 611
           Q+  W   YR+ I
Sbjct: 600 QVDQWLREYRVQI 612


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: 1125
Number of extensions: 43
Number of successful extensions: 3
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: 614
Length of database: 613
Length adjustment: 37
Effective length of query: 577
Effective length of database: 576
Effective search space:   332352
Effective search space used:   332352
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: 53 (25.0 bits)

Align candidate WP_013074357.1 BTUS_RS01465 (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.703163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-159  518.5   0.0   1.4e-159  518.3   0.0    1.0  1  NCBI__GCF_000092905.1:WP_013074357.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092905.1:WP_013074357.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.3   0.0  1.4e-159  1.4e-159       1     517 []       2     534 ..       2     534 .. 0.96

  Alignments for each domain:
  == domain 1  score: 518.3 bits;  conditional E-value: 1.4e-159
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek...e 70 
                                           Cgiag++d + +++e++  +k+m++++  RGPDaeg+w++    +a+l+hrRL+iid ++gaQP+  ++   +
  NCBI__GCF_000092905.1:WP_013074357.1   2 CGIAGWIDWNVEMTEQRPVLKAMADVQYWRGPDAEGIWMS---RRAGLAHRRLSIIDPEGGAQPMIRRHgerT 71 
                                           ****************************************...6*********************99888889 PP

                             TIGR01536  71 vvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrl 143
                                            viv+nGE+YN  eL++ele  Gy+F t++DtEV+L ay +wg ++ver++G +A+ +wde+++elflaRDrl
  NCBI__GCF_000092905.1:WP_013074357.1  72 LVIVYNGELYNMAELQRELEGLGYTFATRCDTEVVLVAYAHWGPACVERFNGIYAIGIWDEQSQELFLARDRL 144
                                           9************************************************************************ PP

                             TIGR01536 144 GikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal...dge 212
                                           G+kPL+ya  ++ l+faSE+K+lla++++++e+d e+lae++++   +++++ +f++  e++p+ al   +  
  NCBI__GCF_000092905.1:WP_013074357.1 145 GVKPLFYAPLASGLVFASELKGLLAHPAVRPEVDSEGLAEIFAMGpGRTPGHGVFRNTCEVKPGWALlfdRRG 217
                                           *********************************************9999*****************9997555 PP

                             TIGR01536 213 ekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak....sevk 281
                                            + ++yw++e++ +++++e++++++r+lled v ++l++dvpv++llSGGlDSs+++a a++ ++     +++
  NCBI__GCF_000092905.1:WP_013074357.1 218 LHHRQYWKLESRPHEDDLETTIATVRDLLEDTVGRQLMSDVPVCTLLSGGLDSSAITAFAARAFRrqgrPPLR 290
                                           55566*******************************************************99999999999** PP

                             TIGR01536 282 tFsigfe.dskdldesk........aarkvadelgtehkevliseeevlkeleevilaleeptairasiplyl 345
                                           tFsi++  ++  ++ ++        +a++vad+l ++ + v++++++v+++l+e ++a + p  +    +l+l
  NCBI__GCF_000092905.1:WP_013074357.1 291 TFSIDYVdNDVYFQPNAfqpaadgpWAERVADFLQVDRRIVTLTPAAVADALREAVRARDLPGMTDIDSSLLL 363
                                           ******96667777665999******************************************96666556666 PP

                             TIGR01536 346 lsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkaklee 418
                                            +++++++  +V+LsGe+aDE+fgGY +f++ +a ea  +p++ +++e+  +l+  + ++++ +++++++++e
  NCBI__GCF_000092905.1:WP_013074357.1 364 FCREIKKE-ATVALSGECADEVFGGYPWFHRKEALEADVFPWSLKMRERISVLHPDFVDHVQPEQYVRRRYRE 435
                                           66666665.***********************9999999********************************** PP

                             TIGR01536 419 elkekeelkkelkeeseleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklrdg 491
                                            l  + +l++e +++ +++e+++l+l  +++ ll++kDr+sma +lEvRvPf+D++lve+++++p+++k+ +g
  NCBI__GCF_000092905.1:WP_013074357.1 436 VLDAVPRLTGENPQDARIREMFYLNLFHWMPVLLDRKDRMSMAVGLEVRVPFCDHRLVEYMWNVPWSIKMAAG 508
                                           ************************************************************************* PP

                             TIGR01536 492 keKvlLreaaeellPeeileRkKeaf 517
                                           +eK lLr a+++llP++ l+RkK++f
  NCBI__GCF_000092905.1:WP_013074357.1 509 REKGLLRLAMKGLLPDDALWRKKSPF 534
                                           ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (613 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 35.36
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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