Alignments for a candidate for asnB in Methylococcus capsulatus str. Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylococcus capsulatus str. Bath

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_010959831.1 MCA_RS02355 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000008325.1:WP_010959831.1
          Length = 624

 Score =  254 bits (650), Expect = 6e-72
 Identities = 214/653 (32%), Positives = 303/653 (46%), Gaps = 68/653 (10%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLM----RHRGPDESGTWHAVDGASGGVVF 56
           MCG+       +G    EG    SA+ R+   M     HRGPD+SG         G  VF
Sbjct: 1   MCGI-------SGLVQLEGVADTSAMRRSVETMVKALAHRGPDDSGV-----AGDGSAVF 48

Query: 57  GFNRLSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAV-FATDGD 115
           G  RL+I       QP+     +A    ++V NGEI N+ ELR  L  +  AV  ATD  
Sbjct: 49  GMARLAIRGCHDGRQPM----VDAETGVMMVCNGEIDNHAELRGWLAERGRAVEHATD-- 102

Query: 116 GEAILAG-YHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVA 174
             A++ G Y   G   ++RL G FA A+WD     L  ARD  G +PLF A   G  + A
Sbjct: 103 -VAVIPGLYLELGDGFVERLVGAFALAVWDPRRGRLLLARDRAGERPLFYACRDGRVSFA 161

Query: 175 SEKKCLLDLVELVGFDTE---IDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRAD 231
           S+   L      V    E    D  A+Q +    Y   P +   G+R++  G   RI  D
Sbjct: 162 SQAAAL------VAGSPEPYPADEAAVQAFLKAGYFEAPASPFAGMRKVLPG--ERIAID 213

Query: 232 QLAPVITRYFVPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDST 291
                 +RY+   F   P   +      DE  AV  ++V +    +V  GAFLSGG+DS+
Sbjct: 214 VKGVERSRYWRLNFTRGPARKNP----LDEFDAVFREAVRRQSEVEVDFGAFLSGGVDSS 269

Query: 292 AIAAL--AIRHNPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPE 349
            + A+  ++  + +L  F   F    + E   A   AE++G  +    V  ++F   L +
Sbjct: 270 LVTAVMRSVHPDRKLKAFGLRFSESSYDEGVFAERVAESLGVDYTPIWVRPEDFPETLAD 329

Query: 350 IVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPFDYLP 409
           +V    EP+ADPA VP   +AR A   V+V L GEGADELFGGY  Y        +  LP
Sbjct: 330 LVRQSGEPLADPAWVPTALLARRASDEVRVALVGEGADELFGGYPTYFGARLAERYSRLP 389

Query: 410 KPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGFRPDWTH 469
             LR  + K  +  P   +  ++    S  L+    G+   F     R VL      WT 
Sbjct: 390 GGLRALIRKAVEAWPVSDKKVTV----SFLLKRFVQGDELDFLA---RHVL------WTS 436

Query: 470 T---------DVTAPVYAESAGWDP--VARMQHIDLFTWLRGDILVKADKITMANSLELR 518
           +          VT P     AG     + R+Q  DL T L   +L KAD+ +M ++LELR
Sbjct: 437 SIPPALLRRLGVTPPETPHVAGPQETMLDRLQQHDLETSLAEGLLTKADRASMRSALELR 496

Query: 519 VPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRA 578
            PFLD +V   A+ LP   ++    TK  L+R     +P  +++R K G  VP+  WLR 
Sbjct: 497 APFLDKDVIEFAATLPERERVQGLETKVFLKRVALRYLPKDIVYRKKRGLSVPLSAWLR- 555

Query: 579 GELLEWAYATVGSSQAGHL-VDIAAVYRMLDEHRCGSSDHSRRLWTMLIFMLW 630
           G L +WA A + S +   L ++ AA   +L EH   S+DH+R LWT+++   W
Sbjct: 556 GPLHDWAEARISSPRLEELGINRAAALELLREHERRSADHARALWTLIVVSEW 608


Lambda     K      H
   0.323    0.138    0.428 

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: 969
Number of extensions: 51
Number of successful extensions: 7
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: 652
Length of database: 624
Length adjustment: 38
Effective length of query: 614
Effective length of database: 586
Effective search space:   359804
Effective search space used:   359804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

Align candidate WP_010959831.1 MCA_RS02355 (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.332004.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-112  360.9   0.0   8.7e-112  360.6   0.0    1.1  1  NCBI__GCF_000008325.1:WP_010959831.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010959831.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.6   0.0  8.7e-112  8.7e-112       1     516 [.       2     545 ..       2     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 360.6 bits;  conditional E-value: 8.7e-112
                             TIGR01536   1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.e 70 
                                           Cgi g+v+l+  a++   ++ ++ m+++lahRGPD++gv  d     a++g +RLai   ++g+QP+ +++  
  NCBI__GCF_000008325.1:WP_010959831.1   2 CGISGLVQLEGVADTsaMRRSVETMVKALAHRGPDDSGVAGD---GSAVFGMARLAIRGCHDGRQPMVDAEtG 71 
                                           **********9999988899******************8666...9**********************99999 PP

                             TIGR01536  71 vvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrl 143
                                           v++v+nGEI Nh eLr  l e+G   e  +D  Vi  +y e+g  +verL G FA+a+wd ++g+l+laRDr 
  NCBI__GCF_000008325.1:WP_010959831.1  72 VMMVCNGEIDNHAELRGWLAERGRAVEHATDVAVIPGLYLELGDGFVERLVGAFALAVWDPRRGRLLLARDRA 144
                                           9************************************************************************ PP

                             TIGR01536 144 GikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgee 213
                                           G +PL+ya+ +g++ faS + al+a    +   d++a++ +l+  + + + + f++++++ p++      +  
  NCBI__GCF_000008325.1:WP_010959831.1 145 GERPLFYACRDGRVSFASQAAALVAGSPEPYPADEAAVQAFLKAGYFEAPASPFAGMRKVLPGERIaidVKGV 217
                                           ************************999555556666666666777999****************998853444 PP

                             TIGR01536 214 kleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.sevktFsi 285
                                           ++++yw+++ ++  +  ++  +e++  +++av+++   +v  g++lSGG+DSslv+a+++  ++ +++k F +
  NCBI__GCF_000008325.1:WP_010959831.1 218 ERSRYWRLNFTRGPA-RKNPLDEFDAVFREAVRRQSEVEVDFGAFLSGGVDSSLVTAVMRSVHPdRKLKAFGL 289
                                           5556******99655.578899****************************************99999****** PP

                             TIGR01536 286 gfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVv 358
                                           +f  ++++de  +a++va+ lg++++ + + +e++ + l++++++  ep+a++a +p+ ll+++a+++ v+V+
  NCBI__GCF_000008325.1:WP_010959831.1 290 RFS-ESSYDEGVFAERVAESLGVDYTPIWVRPEDFPETLADLVRQSGEPLADPAWVPTALLARRASDE-VRVA 360
                                           ***.9*************************************************************99.**** PP

                             TIGR01536 359 LsGeGaDElfgGYeyfreakaeeale............lpeaselaekkl....................... 396
                                           L GeGaDElfgGY  ++ a  +e+                         +                       
  NCBI__GCF_000008325.1:WP_010959831.1 361 LVGEGADELFGGYPTYFGARLAERYSrlpgglralirkA----------Veawpvsdkkvtvsfllkrfvqgd 423
                                           **************9999887776665555544433330..........123342223333444444433333 PP

                             TIGR01536 397 ...llqaklakeselkellkakleeelkekeelkkelkee....................seleellrldlel 446
                                              +l++++  +s+                         +                    + l++l+++dle+
  NCBI__GCF_000008325.1:WP_010959831.1 424 eldFLARHVLWTSSIPP----------------------AllrrlgvtppetphvagpqeTMLDRLQQHDLET 474
                                           33322222222222222......................222233333333344566666999********** PP

                             TIGR01536 447 llsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                            l + l+ k Dr+sm   lE+R+PflDk+++e+a+++p   +++  ++Kv L+++a ++lP++i++RkK++
  NCBI__GCF_000008325.1:WP_010959831.1 475 SLAEGLLTKaDRASMRSALELRAPFLDKDVIEFAATLPERERVQGLETKVFLKRVALRYLPKDIVYRKKRG 545
                                           **99999999***********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (624 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 43.76
//
[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