Alignments for a candidate for asnB in Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_012281454.1 HM1_RS01365 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000019165.1:WP_012281454.1
          Length = 614

 Score =  701 bits (1810), Expect = 0.0
 Identities = 336/613 (54%), Positives = 422/613 (68%), Gaps = 2/613 (0%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDIEGGR 60
           MCGI GWVD++  L Q+   +D M +TL+ RGPD S  W     L GH+RL+VVD  GG 
Sbjct: 1   MCGIVGWVDWEADLSQQGTILDAMVETLTHRGPDASGTWISPQALIGHRRLSVVDRIGGV 60

Query: 61  QPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVDH 120
           QPM     G  Y + YNGELYNT +LR+EL  RGH+F   SDTE LL ++IEW EDCV  
Sbjct: 61  QPMIREVGGRRYVLTYNGELYNTPELRQELEVRGHRFRTRSDTEALLLAFIEWGEDCVQK 120

Query: 121 LNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDRT 180
           LNGIFAF VWDE    LF ARDR+GVKP FY + GS+ LF SE+KA+LAHPDI+  +D  
Sbjct: 121 LNGIFAFGVWDETERRLFLARDRMGVKPLFYVRRGSALLFASELKALLAHPDIRPELDAE 180

Query: 181 GLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWRYWNVESEKHTDSFDDTVA 240
           GL+E+F + P+RTPG G+FKGI+E+RP + LT     +    YW ++S  H D+ + T  
Sbjct: 181 GLAEVFAIAPARTPGHGVFKGIQEVRPGYTLTIDAASMRKKPYWTLKSRPHEDNLEQTTE 240

Query: 241 NVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSIDYEEND 300
            +R L  DA+ RQLVSDVPVCT LSGGLDSS +TA+AA  + ++G  PL+TYSIDY +ND
Sbjct: 241 RLRELLLDAIERQLVSDVPVCTLLSGGLDSSTLTAVAAHVYARDGLGPLNTYSIDYRDND 300

Query: 301 KYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMADVDSS 360
            YF+ SAFQPN D PWI++++   GT HH  +I   +LVD L  A+  +DLPGMADV+SS
Sbjct: 301 IYFKPSAFQPNADAPWIKRVSAHLGTVHHDVIIDTPELVDALRPALWARDLPGMADVESS 360

Query: 361 LLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADV--ESGFPWMRSTEERIKLLSDSWQ 418
           L  FCREIKK   V+LSGECADE+FGGYPWFH  ++     FPW R   ER  LL+   +
Sbjct: 361 LYLFCREIKKGATVALSGECADEVFGGYPWFHRPELLNVGTFPWSRRLAERADLLAPEMR 420

Query: 419 KKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMTNLLDRKDRMSMGAS 478
           + +  + YV  +YEETLAE P L GE   +  RR++FYLN+ WFM  LLDRKDRMSM   
Sbjct: 421 QYIQPEAYVARRYEETLAEVPRLPGEDAEEARRREMFYLNIHWFMATLLDRKDRMSMAHG 480

Query: 479 LEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDILYRKKSPYPKTHHP 538
           LEVRVPF DHR+VEYVWNIPW MK  + REKG+LR+AL GILP+D+L+RKKSPYPKTHHP
Sbjct: 481 LEVRVPFCDHRIVEYVWNIPWAMKTCEGREKGLLRRALRGILPEDVLWRKKSPYPKTHHP 540

Query: 539 EYTKGVSEWLKTIRSQKDSVLHTLLDRKQLDQLLETEGSSFKVPWFGQLMKGPQLIAHLA 598
            YT  V +WL  I     S L  ++D +++  L   +  +  +PWFGQLM  PQL A+LA
Sbjct: 541 AYTAAVRQWLTEILHDPASPLLPIIDVEKVRALAAADAVTTDLPWFGQLMGLPQLYAYLA 600

Query: 599 QIHTWFEAYRIDI 611
           Q+  W    +I I
Sbjct: 601 QVDLWLRTMQISI 613


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: 1137
Number of extensions: 47
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: 614
Length of database: 614
Length adjustment: 37
Effective length of query: 577
Effective length of database: 577
Effective search space:   332929
Effective search space used:   332929
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_012281454.1 HM1_RS01365 (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.1459677.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-166  540.1   0.0     4e-166  539.9   0.0    1.0  1  NCBI__GCF_000019165.1:WP_012281454.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019165.1:WP_012281454.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.9   0.0    4e-166    4e-166       1     517 []       2     534 ..       2     534 .. 0.97

  Alignments for each domain:
  == domain 1  score: 539.9 bits;  conditional E-value: 4e-166
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek...e 70 
                                           Cgi+g+vd +a+++++   +++m+etl hRGPDa+g+w++    +a++ghrRL+++d  +g QP+  e    +
  NCBI__GCF_000019165.1:WP_012281454.1   2 CGIVGWVDWEADLSQQGTILDAMVETLTHRGPDASGTWIS---PQALIGHRRLSVVDRIGGVQPMIREVggrR 71 
                                           ***************99***********************...69*********************9999999 PP

                             TIGR01536  71 vvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrl 143
                                           +v+++nGE+YN+ eLr+ele +G++F+t+sDtE +L a+ ewge++v++L+G FAf +wde +++lflaRDr+
  NCBI__GCF_000019165.1:WP_012281454.1  72 YVLTYNGELYNTPELRQELEVRGHRFRTRSDTEALLLAFIEWGEDCVQKLNGIFAFGVWDETERRLFLARDRM 144
                                           ************************************************************************* PP

                             TIGR01536 144 GikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal...dge 212
                                           G+kPL+y + +++llfaSE+Kalla+++i++eld+e+lae++++   +++++ +fk+++e++p+  l     +
  NCBI__GCF_000019165.1:WP_012281454.1 145 GVKPLFYVRRGSALLFASELKALLAHPDIRPELDAEGLAEVFAIApARTPGHGVFKGIQEVRPGYTLtidAAS 217
                                           *********************************************999*******************874344 PP

                             TIGR01536 213 eklee.ywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak....sev 280
                                            ++ + yw ++++ +++++e+++e+lrell da++++lv+dvpv++llSGGlDSs+++a+a++  +    +++
  NCBI__GCF_000019165.1:WP_012281454.1 218 MRK-KpYWTLKSRPHEDNLEQTTERLRELLLDAIERQLVSDVPVCTLLSGGLDSSTLTAVAAHVYArdglGPL 289
                                           444.35*********************************************************99999***** PP

                             TIGR01536 281 ktFsigfe.dskdldesk........aarkvadelgtehkevliseeevlkeleevilaleeptairasiply 344
                                           +t+si++  ++  ++ s+        ++++v+++lgt h+ v+i+  e++++l+  ++a + p       +ly
  NCBI__GCF_000019165.1:WP_012281454.1 290 NTYSIDYRdNDIYFKPSAfqpnadapWIKRVSAHLGTVHHDVIIDTPELVDALRPALWARDLPGMADVESSLY 362
                                           ********888889988899********************************************999999*** PP

                             TIGR01536 345 llsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakle 417
                                           l ++++++   +V+LsGe+aDE+fgGY +f++++  +   +p++++lae++ ll+ ++++  + + ++ +++e
  NCBI__GCF_000019165.1:WP_012281454.1 363 LFCREIKKG-ATVALSGECADEVFGGYPWFHRPELLNVGTFPWSRRLAERADLLAPEMRQYIQPEAYVARRYE 434
                                           *99999887.***********************9999999********************************* PP

                             TIGR01536 418 eelkekeelkkelkeeseleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklrd 490
                                           e+l+e+ +l +e +ee + +e+++l++++++  ll++kDr+smah+lEvRvPf+D+++ve++++ip+ +k+ +
  NCBI__GCF_000019165.1:WP_012281454.1 435 ETLAEVPRLPGEDAEEARRREMFYLNIHWFMATLLDRKDRMSMAHGLEVRVPFCDHRIVEYVWNIPWAMKTCE 507
                                           ************************************************************************* PP

                             TIGR01536 491 gkeKvlLreaaeellPeeileRkKeaf 517
                                           g+eK lLr+a++++lPe++l+RkK+++
  NCBI__GCF_000019165.1:WP_012281454.1 508 GREKGLLRRALRGILPEDVLWRKKSPY 534
                                           ************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (614 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.30
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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