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 asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_010959890.1 MCA_RS02680 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000008325.1:WP_010959890.1
          Length = 606

 Score =  224 bits (572), Expect = 6e-63
 Identities = 170/564 (30%), Positives = 271/564 (48%), Gaps = 51/564 (9%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDIEGGR 60
           MCGI G   F   L  ++  +D+    L+ RGPDD  ++ +     GH RL+++D+ GG 
Sbjct: 1   MCGIAGL--FNCNLPADELRLDQAVAKLTHRGPDDRGIFLDGRFGMGHTRLSIIDLAGGH 58

Query: 61  QPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVDH 120
           QP+    +     +I NGE+YN  +LR EL A G +F+  SD+EV+LH+Y+ + E  ++ 
Sbjct: 59  QPLFSEDR--RLALIANGEIYNFIELRSELTAAGFRFQTQSDSEVILHAYLAFGEGFLER 116

Query: 121 LNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDRT 180
           + G+FAFA++D     L  ARDRLG+KP F  +      F SEIKA+L   D    +D  
Sbjct: 117 IQGMFAFALYDALEGRLILARDRLGIKPLFLARRPDGIAFASEIKALLPLLDQPREIDPQ 176

Query: 181 GLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTF-SKDGLNIWRYWNVESEKHTD-SFDDT 238
           GL++ F      T  T + +G++ + P  A+   +      +RYW+  + +  +  FD+ 
Sbjct: 177 GLAQYF-QNQFSTGATTVLRGVERVLPGEAVVVEAGKTTRRFRYWSPLAVRTEELDFDEA 235

Query: 239 VANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSIDYEE 298
            A   +L +  +   + SDVP   FLSGG+DSS + A+      +    P+ T+S+ +  
Sbjct: 236 AARFDALMERVMVEHMRSDVPFGLFLSGGVDSSLLLAL----LTRYSGEPIRTFSVGFPG 291

Query: 299 NDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKD--LPGMAD 356
                        D+ P  E +   F + H +     +D++  L   V   D  +   A 
Sbjct: 292 TSL---------TDELPLAEGLARRFRSRHREIRPGPQDILHSLPLTVWAADDLMRDNAS 342

Query: 357 VDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVESGF-----PWMRSTEERIK 411
           + +SLL   R   ++  V  SGE  DE+F GY  + T+ +E  F     P       R  
Sbjct: 343 LPTSLL--ARAAGEELKVVFSGEGGDEVFAGYGRYRTSPLERLFKSLLAPGSGGFRTR-G 399

Query: 412 LLSDSWQKK------LNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFM-T 464
                W K       L   +      +E+  ETP        D  R Q  Y+++   +  
Sbjct: 400 SFRGRWPKTLFGPALLAAAQSARRPVQESWRETP----REWSDLQRMQ--YVDLCHALPD 453

Query: 465 NLLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDI 524
           NLL + DRM M   +E RVPF DHR+VE+  ++P  +K+   + K  L++  E ++P + 
Sbjct: 454 NLLVKADRMLMAWGVEGRVPFLDHRVVEFGLSLPDRLKIEGRQGKLFLKRWGERLVPAEQ 513

Query: 525 LYRKKSPYPKTHHPEYTKGVSEWL 548
           LY +K  +   H P     + EWL
Sbjct: 514 LYARKRGF---HVP-----LGEWL 529


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: 919
Number of extensions: 51
Number of successful extensions: 5
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: 614
Length of database: 606
Length adjustment: 37
Effective length of query: 577
Effective length of database: 569
Effective search space:   328313
Effective search space used:   328313
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_010959890.1 MCA_RS02680 (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.1210105.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-138  447.7   0.0   3.9e-138  447.5   0.0    1.0  1  NCBI__GCF_000008325.1:WP_010959890.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010959890.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.5   0.0  3.9e-138  3.9e-138       1     517 []       2     521 ..       2     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 447.5 bits;  conditional E-value: 3.9e-138
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgiag+++ +  a+e    +++ + +l hRGPD++g++ d    + ++gh RL+iidl +g+QPl +e+ + +
  NCBI__GCF_000008325.1:WP_010959890.1   2 CGIAGLFNCNLPADE--LRLDQAVAKLTHRGPDDRGIFLD---GRFGMGHTRLSIIDLAGGHQPLFSEDrRLA 69 
                                           *********887777..457777889**************...8**************************9** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           ++ nGEIYN+ eLr el ++G++F+t+sD+EViL+ay ++ge ++er++GmFAfal+d+ +g+l+laRDrlGi
  NCBI__GCF_000008325.1:WP_010959890.1  70 LIANGEIYNFIELRSELTAAGFRFQTQSDSEVILHAYLAFGEGFLERIQGMFAFALYDALEGRLILARDRLGI 142
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal....dgeek 214
                                           kPL+ a+  + ++faSEiKall+l + ++e+d ++la++++ q+++  +t+ ++v+++ p++a+     ++++
  NCBI__GCF_000008325.1:WP_010959890.1 143 KPLFLARRPDGIAFASEIKALLPLLDQPREIDPQGLAQYFQNQFSTGATTVLRGVERVLPGEAVvveaGKTTR 215
                                           *******************************************99******************9886544444 PP

                             TIGR01536 215 leeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsig 286
                                           + +yw+    +  + +++e+ ++++ l+e+   +++++dvp g++lSGG+DSsl+ a++ +++ ++++tFs+g
  NCBI__GCF_000008325.1:WP_010959890.1 216 RFRYWSPLAVRtEELDFDEAAARFDALMERVMVEHMRSDVPFGLFLSGGVDSSLLLALLTRYSGEPIRTFSVG 288
                                           45599976666488899******************************************************** PP

                             TIGR01536 287 fedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvL 359
                                           f++ +  de   a+ +a+ ++++h+e+   ++++l+ l+  ++a ++++ ++as p+ ll+++a e+ +kVv+
  NCBI__GCF_000008325.1:WP_010959890.1 289 FPGTSLTDELPLAEGLARRFRSRHREIRPGPQDILHSLPLTVWAADDLMRDNASLPTSLLARAAGEE-LKVVF 360
                                           *****************************************************************99.***** PP

                             TIGR01536 360 sGeGaDElfgGYeyfreakaeealelpease..laekklllqaklakeselkellkakleeelkekeelkkel 430
                                           sGeG+DE+f+GY ++r+++ e+ ++   a      +++   + ++ k+     ll a   ++++ ++e  +e+
  NCBI__GCF_000008325.1:WP_010959890.1 361 SGEGGDEVFAGYGRYRTSPLERLFKSLLAPGsgGFRTRGSFRGRWPKTLFGPALLAAAQ-SARRPVQESWRET 432
                                           ************************93333332222222233334444444444444333.3333344444444 PP

                             TIGR01536 431 kee.seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaa 501
                                           ++e s+l+++++ dl   l+d+l++k Dr++ma+++E RvPflD+++ve+ ls+p  lk++  + K  L++  
  NCBI__GCF_000008325.1:WP_010959890.1 433 PREwSDLQRMQYVDLCHALPDNLLVKaDRMLMAWGVEGRVPFLDHRVVEFGLSLPDRLKIEGRQGKLFLKRWG 505
                                           4447********************************************************************* PP

                             TIGR01536 502 eellPeeileRkKeaf 517
                                           e+l+P e l+ +K++f
  NCBI__GCF_000008325.1:WP_010959890.1 506 ERLVPAEQLYARKRGF 521
                                           *******999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (606 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: 00:00:00.01
# Mc/sec: 30.48
//
[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