Alignments for a candidate for asnB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sinorhizobium meliloti 1021

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate SM_b20481 SM_b20481 asparagine synthetase (glutamine amidotransferase) protein

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__Smeli:SM_b20481
          Length = 591

 Score =  254 bits (648), Expect = 1e-71
 Identities = 192/632 (30%), Positives = 307/632 (48%), Gaps = 71/632 (11%)

Query: 1   MCGFVGV--FNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDV 58
           MCG  G   F+    + TA     +  M  ++  RGPD+ G     +VG G RRL I+D+
Sbjct: 1   MCGICGEVRFDGGSPSVTA-----VSIMADVLAPRGPDASGVVVRGNVGLGHRRLRILDL 55

Query: 59  -ENGGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
            +   QP+   D    ++FNG IYN+ ELR ELE KGY F +  DTEV+L  +  + EE 
Sbjct: 56  SDKSQQPMVDSDLGLSLVFNGCIYNFRELRLELEEKGYRFFSSGDTEVILKAWHAWGEEC 115

Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DIEI 176
            S+  GMFAF+I  ++   +  ARD FGIKPLY   +   + FAS   +L+ A   D  I
Sbjct: 116 VSRFHGMFAFVIHERDSGRVVMARDRFGIKPLYIAEVQGALRFASALPALVKAGGVDTSI 175

Query: 177 DKEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFK----PVQ 231
           D  AL  YM+F   VP P T+   V+K+ P +      DG    + Y+   ++       
Sbjct: 176 DVAALHNYMTFHAVVPPPRTILNGVRKLPPATLRVYERDGSFEDRRYWDPPYRRQAGDAA 235

Query: 232 TEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGF 290
              ++  +++ DA+  +V   M +DVPVG  LSGG+DSS IV  +A+     L +FSVGF
Sbjct: 236 ISREEWQEQLLDALRIAVKRRMVADVPVGVLLSGGVDSSLIVGLLAEAGQRGLMSFSVGF 295

Query: 291 EQQGFSEVD---VAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYF 347
           E+    + D    +   A   G ++    +   + M  LP  +    +P+     +  Y 
Sbjct: 296 EEANGEKGDEFVYSDLIAGHFGTDHRKIFVPSADLMGALPGTIAAMSEPMVSYDNVGFYL 355

Query: 348 VAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMR 407
           ++KE  KHV V  SG+GADE+FGGY+ Y                   L++   V+ +   
Sbjct: 356 LSKEVSKHVKVVQSGQGADEVFGGYHWY-----------------PPLMNSNDVVAD--Y 396

Query: 408 GKSLLERG----CTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYS 463
           GK+  +R      T L D +I +  +  + + + LL+                    + +
Sbjct: 397 GKAFRDRSHAVLTTQLSDAWIADHDVSGDLLNEHLLR------------------EGAAT 438

Query: 464 DINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTT 523
            +++   +D +  +  D + + D MTMA  LE RVPFLD  + ++A+++P E K ++G  
Sbjct: 439 PVDQALRLDSNVMLVDDPVKRVDNMTMAWGLEARVPFLDHELVELAARMPPEEKLRDG-G 497

Query: 524 KYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQT-------DAYI 576
           K +L+  A  ++P  V++RKK  FPVP   ++     + +R+ ++  +        DAY+
Sbjct: 498 KGILKDVARRVIPSEVIDRKKGYFPVPQLKYIAGPYLDLIRDTLRSQKARERGLFQDAYL 557

Query: 577 HKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608
             D + Q   DH         ++W V +  +W
Sbjct: 558 --DRLFQEPSDHITPL--RGSELWQVGLLEMW 585


Lambda     K      H
   0.319    0.136    0.403 

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: 886
Number of extensions: 47
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: 632
Length of database: 591
Length adjustment: 37
Effective length of query: 595
Effective length of database: 554
Effective search space:   329630
Effective search space used:   329630
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate SM_b20481 SM_b20481 (asparagine synthetase (glutamine amidotransferase) protein)
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.5416.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.3e-133  430.6   0.0   6.1e-133  430.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20481  SM_b20481 asparagine synthetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20481  SM_b20481 asparagine synthetase (glutamine amidotransferase) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.4   0.0  6.1e-133  6.1e-133       1     516 [.       2     520 ..       2     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 430.4 bits;  conditional E-value: 6.1e-133
                            TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evv 72 
                                          Cgi g v  +  + +   a++ m+++la RGPDa+gv       n++lghrRL i dls++ +QP+ + +    
  lcl|FitnessBrowser__Smeli:SM_b20481   2 CGICGEVRFDGGSPS-VTAVSIMADVLAPRGPDASGVVVR---GNVGLGHRRLRILDLSDKsQQPMVDSDlGLS 71 
                                          9*******9887555.689*****************8666...9****************99*********99* PP

                            TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGik 146
                                          +vfnG IYN++eLr eleekGy+F +  DtEViL+a+++wgee+v+r++GmFAf+++++ +g++++aRDr+Gik
  lcl|FitnessBrowser__Smeli:SM_b20481  72 LVFNGCIYNFRELRLELEEKGYRFFSSGDTEVILKAWHAWGEECVSRFHGMFAFVIHERDSGRVVMARDRFGIK 145
                                          ************************************************************************** PP

                            TIGR01536 147 PLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal..dgeeklee 217
                                          PLY a+ qg+l faS + al+++  +++++d +al++++t++ +vp+++t+ ++v++l+pa  +  + + ++e+
  lcl|FitnessBrowser__Smeli:SM_b20481 146 PLYIAEVQGALRFASALPALVKAGGVDTSIDVAALHNYMTFHaVVPPPRTILNGVRKLPPATLRvyERDGSFED 219
                                          ******************************************999****************9999844455554 PP

                            TIGR01536 218 ..ywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsi 285
                                            yw+  +++     + s ee  e+l ++l+ avk+r+vadvpvgvllSGG+DSsl++ ++++  ++ + +Fs+
  lcl|FitnessBrowser__Smeli:SM_b20481 220 rrYWDPPYRRqagdAAISREEWQEQLLDALRIAVKRRMVADVPVGVLLSGGVDSSLIVGLLAEAGQRGLMSFSV 293
                                          55****99997777778899999*************************************************** PP

                            TIGR01536 286 gfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkV 357
                                          gfe  + ++ de  +   +a ++gt+h+++ + +++++ +l+  i a+ ep+   + ++ yllsk+++++ vkV
  lcl|FitnessBrowser__Smeli:SM_b20481 294 GFEeaNGEKGDEFVYSDLIAGHFGTDHRKIFVPSADLMGALPGTIAAMSEPMVSYDNVGFYLLSKEVSKH-VKV 366
                                          ***66667777788********************************************************.*** PP

                            TIGR01536 358 vLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakleeelkekeelkkelk 431
                                          v sG+GaDE+fgGY+++    +++++   + + ++ +++   a l+++ +++ ++ ++++ +l + + l +   
  lcl|FitnessBrowser__Smeli:SM_b20481 367 VQSGQGADEVFGGYHWYPPLMNSNDVVADYGKAFRDRSH---AVLTTQLSDAWIADHDVSGDLLNEHLLRE--G 435
                                          ********************9999997444444444333...33444444444444444444444443333..3 PP

                            TIGR01536 432 eeseleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeel 504
                                          +++ ++++lrld + +l d+ +++ D ++ma++lE+RvPflD+elvela+++ppe klrdg  K +L+ +a+++
  lcl|FitnessBrowser__Smeli:SM_b20481 436 AATPVDQALRLDSNVMLVDDpVKRVDNMTMAWGLEARVPFLDHELVELAARMPPEEKLRDG-GKGILKDVARRV 508
                                          3478999999999988877626666**********************************98.79********** PP

                            TIGR01536 505 lPeeileRkKea 516
                                          +P+e+ +RkK  
  lcl|FitnessBrowser__Smeli:SM_b20481 509 IPSEVIDRKKGY 520
                                          *********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (591 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.08
//
[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