Alignments for a candidate for asnB in Roseburia faecis M72

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Roseburia faecis M72

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_055067462.1 M72_RS05350 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_001406815.1:WP_055067462.1
          Length = 615

 Score =  605 bits (1559), Expect = e-177
 Identities = 300/617 (48%), Positives = 411/617 (66%), Gaps = 8/617 (1%)

Query: 1   MCGITGWVDFKKQLVQEKQTMD----RMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI 56
           MCGI+G+ DF      +K   +    +M +TL  RGPD + +  + HV   H RL++ D+
Sbjct: 1   MCGISGFCDFSLNYYDKKTFWETILVQMHETLKHRGPDQAMIDLQPHVGLSHARLSIRDL 60

Query: 57  EGGRQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQED 116
           + G QPM  T+ G T +I+YNGE+YN  +L  EL+A G++F  TSDTE++L +Y+ + ++
Sbjct: 61  KSGIQPMTRTFHGKTCSIVYNGEIYNHRELLPELQAAGYRFTTTSDTEIILCAYMHFGKN 120

Query: 117 CVDHLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKAR 176
            V+ LNGIFAFA+WD+    L   RDR G KP FYT+ GSSF+FGSE KA+  HPD+   
Sbjct: 121 FVEKLNGIFAFAIWDDTTRELLLYRDRAGTKPLFYTQTGSSFVFGSEPKALFCHPDVTPS 180

Query: 177 VDRTGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWRYWNVESEKHTDSFD 236
           +D+  L EI  +GP+RT G G+F G+KE+ P H   F  DG +   YW++   +H DS+ 
Sbjct: 181 IDKNSLQEILAVGPARTYGNGVFTGVKEVMPGHYHIFCPDGQHDILYWDLPCREHKDSYA 240

Query: 237 DTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSIDY 296
            TV  V  L +D V RQ+VSDVPVCTFLSGG+DSS +TA+AA H +KEGK  L+T+S D+
Sbjct: 241 QTVQTVSFLVRDTVERQMVSDVPVCTFLSGGIDSSIVTALAARHMQKEGKI-LNTFSFDF 299

Query: 297 EENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMAD 356
            EN+KYF+++AFQP  D P++ +M +   T+H     SQ+ L   L +AV  KDLPGM D
Sbjct: 300 SENEKYFKSNAFQPERDLPYVNRMLQYCKTSHTYLECSQEALFAALSDAVTAKDLPGMTD 359

Query: 357 VDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADV--ESGFPWMRSTEERIKLLS 414
           VD+SLL+FC E+ K   V+L+GECADEIFGGYPWF+  ++    GFPW      R  +LS
Sbjct: 360 VDASLLYFCSEVAKHNKVTLTGECADEIFGGYPWFYRPELMNRDGFPWSADPAARTSILS 419

Query: 415 DSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMTNLLDRKDRMS 474
           D   + L+L EY +A+YEETL+  P LDGE+  +  RR + YLN+ WFM  LLDR DR S
Sbjct: 420 DDVLRTLDLAEYSHARYEETLSHVPHLDGESPEEARRRDIGYLNIKWFMQTLLDRMDRTS 479

Query: 475 MGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDILYRKKSPYPK 534
           M +SLE RVPFADHR++EYV+N+PW+MK  +  EK +LR A   +LP ++L+RKKSPYPK
Sbjct: 480 MYSSLEARVPFADHRIMEYVFNVPWQMKYRNGVEKSLLRDACADLLPRELLWRKKSPYPK 539

Query: 535 THHPEYTKGVSEWLKTIRSQKDSVLHTLLDRKQLDQLLETEGSSFKVPWFGQLMKGPQLI 594
           T+HP Y + +   ++ I +  +S +  LLDR + +  L       K PWFGQLM GPQLI
Sbjct: 540 TYHPAYEQMLIRRMREILNDPNSPVLPLLDRSKTEAFLAAPKELGK-PWFGQLMAGPQLI 598

Query: 595 AHLAQIHTWFEAYRIDI 611
           A+  QI+TW + Y + I
Sbjct: 599 AYFIQINTWMQIYHLSI 615


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: 1052
Number of extensions: 45
Number of successful extensions: 5
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: 615
Length adjustment: 37
Effective length of query: 577
Effective length of database: 578
Effective search space:   333506
Effective search space used:   333506
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_055067462.1 M72_RS05350 (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.1919171.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-150  488.9   0.0   1.3e-150  488.7   0.0    1.0  1  NCBI__GCF_001406815.1:WP_055067462.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001406815.1:WP_055067462.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.7   0.0  1.3e-150  1.3e-150       1     517 []       2     537 ..       2     537 .. 0.96

  Alignments for each domain:
  == domain 1  score: 488.7 bits;  conditional E-value: 1.3e-150
                             TIGR01536   1 Cgiagivdlkakake....eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                           Cgi g++d + +  +     e  + +m etl+hRGPD+    +d  + +++l h+RL+i dl++g QP+  + 
  NCBI__GCF_001406815.1:WP_055067462.1   2 CGISGFCDFSLNYYDkktfWETILVQMHETLKHRGPDQAM--ID-LQPHVGLSHARLSIRDLKSGIQPMTRTF 71 
                                           ******9987665544346568899*************98..67.689***********************99 PP

                             TIGR01536  70 ...evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelfla 139
                                              +  iv+nGEIYNh+eL  el+++Gy+F+t+sDtE+iL+ay ++g+++ve+L+G FAfa+wd+ ++el+l 
  NCBI__GCF_001406815.1:WP_055067462.1  72 hgkTCSIVYNGEIYNHRELLPELQAAGYRFTTTSDTEIILCAYMHFGKNFVEKLNGIFAFAIWDDTTRELLLY 144
                                           999999******************************************************************* PP

                             TIGR01536 140 RDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal.. 209
                                           RDr G kPL+y++++++++f+SE Kal++++++++++dk+ l+e+l++   ++ ++ +f +vke++p+++   
  NCBI__GCF_001406815.1:WP_055067462.1 145 RDRAGTKPLFYTQTGSSFVFGSEPKALFCHPDVTPSIDKNSLQEILAVGpARTYGNGVFTGVKEVMPGHYHif 217
                                           *************************************************999*******************9* PP

                             TIGR01536 210 ..dgeekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak... 277
                                             dg++++  yw++  +e+k+s  ++v+++  l++d v++++v+dvpv+++lSGG+DSs+v+a+a+++++   
  NCBI__GCF_001406815.1:WP_055067462.1 218 cpDGQHDIL-YWDLPCREHKDSYAQTVQTVSFLVRDTVERQMVSDVPVCTFLSGGIDSSIVTALAARHMQkeg 289
                                           999999999.***********************************************************9998 PP

                             TIGR01536 278 sevktFsigfe.dskdldesk........aarkvadelgtehkevliseeevlkeleevilaleep.tairas 340
                                           + ++tFs +f  ++k +++++        + +++ +++ t+h+ ++ s+e+++++l + + a++ p +++ ++
  NCBI__GCF_001406815.1:WP_055067462.1 290 KILNTFSFDFSeNEKYFKSNAfqperdlpYVNRMLQYCKTSHTYLECSQEALFAALSDAVTAKDLPgMTDVDA 362
                                           889********8889999776*******************************************662666666 PP

                             TIGR01536 341 iplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellk 413
                                             ly++s+ a+++  kV L+Ge+aDE+fgGY +f +++  ++  +p++++ a+++ +l++ + ++ +l+e+ +
  NCBI__GCF_001406815.1:WP_055067462.1 363 SLLYFCSEVAKHN--KVTLTGECADEIFGGYPWFYRPELMNRDGFPWSADPAARTSILSDDVLRTLDLAEYSH 433
                                           7778888888777..********************************************************** PP

                             TIGR01536 414 akleeelkekeelkkelkeeseleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippel 486
                                           a++ee+l+++ +l++e++ee + +++ +l+++++++ ll++ Dr+sm  slE+RvPf+D++++e+++++p+++
  NCBI__GCF_001406815.1:WP_055067462.1 434 ARYEETLSHVPHLDGESPEEARRRDIGYLNIKWFMQTLLDRMDRTSMYSSLEARVPFADHRIMEYVFNVPWQM 506
                                           ************************************************************************* PP

                             TIGR01536 487 klrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           k r+g eK lLr a+++llP+e+l+RkK+++
  NCBI__GCF_001406815.1:WP_055067462.1 507 KYRNGVEKSLLRDACADLLPRELLWRKKSPY 537
                                           ****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (615 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: 33.37
//
[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