Alignments for a candidate for asnA in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnA in Desulfatiglans anilini DSM 4660

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_028322146.1 H567_RS0115785 aspartate--ammonia ligase

Query= BRENDA::A4I213
         (353 letters)



>NCBI__GCF_000422285.1:WP_028322146.1
          Length = 376

 Score =  258 bits (660), Expect = 1e-73
 Identities = 146/350 (41%), Positives = 198/350 (56%), Gaps = 26/350 (7%)

Query: 3   SSPQEYIDLQTRILRVKTIFAEELASALNLIQVECPMLACVGDGTQDNLS--GVEKAVQV 60
           +SP    + Q  I   K    E L   LNL++V  P++  V  G  D L   G    VQ 
Sbjct: 28  ASPLSPRETQEAIYAAKDYIEENLCRQLNLMRVTVPLIVDVDSGVNDYLDRDGSRSPVQF 87

Query: 61  HVKEIPGAN---YEVVHSLAKWKRMTLGNHRFPVGRGIFTNMRALRVEETLDNIHSVYVD 117
           H+      N    ++V +  KWKR+ L       G G+ T+MRA+R +  LD+ HS YVD
Sbjct: 88  HISNDRDKNPVDAQIVQAATKWKRIALRQFGMQFGEGVLTDMRAVRKDYFLDHDHSAYVD 147

Query: 118 QWDWERVIAPADRCLEYLQATVRSLYEVLRETESRLCTEFPDIA----PILPDSIKFVHT 173
           QWDWE  I    R L++L   VR ++ VL+  E  + + FP +     P LPD + F+H 
Sbjct: 148 QWDWEMAITAEQRNLDFLTEVVRRIWTVLKGAEQHVQSLFPALKSSRYPDLPDELTFIHA 207

Query: 174 EQLLKRYPELDPKSREREAVKKLGAVFLIGIGCKLSHGDHHDVRAPDYDDWSSPVSVDSS 233
           E +L+RYP+L  K RE   V++  AVF+ GIG  L  G  H++RA DYDDW++       
Sbjct: 208 EDILERYPDLPRKQRETRIVQEYPAVFIYGIGWVLEDGYPHEMRAADYDDWATET----- 262

Query: 234 KIGFPTADDEKPSVNTIMSLQGLNGDILVYNPVLDDVLELSSMGIRVDQEALRRQLEITG 293
                 + D +P       + GLNGDILV+NPV     EL+SMGIRV+ E LR+QLEI+G
Sbjct: 263 -----VSRDGRP-------MHGLNGDILVWNPVTKRRHELTSMGIRVNAETLRQQLEISG 310

Query: 294 TSDRLQCRWHQCVLNGDLPQTIGGGIGQSRTVMFMLRKRHIGEVQCSVWP 343
             D L+  +HQ VL  ++P +IGGGIGQSRT M +L+K H+GEV  SVWP
Sbjct: 311 QLDLLKMPYHQAVLKNEIPLSIGGGIGQSRTFMLLLQKAHLGEVSVSVWP 360


Lambda     K      H
   0.320    0.136    0.412 

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: 336
Number of extensions: 13
Number of successful extensions: 4
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: 353
Length of database: 376
Length adjustment: 29
Effective length of query: 324
Effective length of database: 347
Effective search space:   112428
Effective search space used:   112428
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: 49 (23.5 bits)

Align candidate WP_028322146.1 H567_RS0115785 (aspartate--ammonia ligase)
to HMM TIGR00669 (asnA: aspartate--ammonia ligase (EC 6.3.1.1))

# 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/TIGR00669.hmm
# target sequence database:        /tmp/gapView.13815.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00669  [M=330]
Accession:   TIGR00669
Description: asnA: aspartate--ammonia ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.7e-97  310.9   0.1    7.5e-97  310.5   0.1    1.0  1  lcl|NCBI__GCF_000422285.1:WP_028322146.1  H567_RS0115785 aspartate--ammoni


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000422285.1:WP_028322146.1  H567_RS0115785 aspartate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.5   0.1   7.5e-97   7.5e-97       9     324 ..      37     365 ..      34     371 .. 0.91

  Alignments for each domain:
  == domain 1  score: 310.5 bits;  conditional E-value: 7.5e-97
                                 TIGR00669   9 qqeisfvkstftqklierlglievqgpilsqvgdgiqdnl..sgiekavqvkvkaipd...aafevvhs 72 
                                               q+ i  +k+ + ++l  +l l+ v  p++  v  g++d l   g    vq ++    d      ++v +
  lcl|NCBI__GCF_000422285.1:WP_028322146.1  37 QEAIYAAKDYIEENLCRQLNLMRVTVPLIVDVDSGVNDYLdrDGSRSPVQFHISNDRDknpVDAQIVQA 105
                                               77888999******************************9843589999999887655411145789*** PP

                                 TIGR00669  73 lakwkrhtlarydfkedeglfvhmkalrpdedsldpvrsvyvdqwdwekvvpegernlaylketveaiy 141
                                                +kwkr +l +++++ +eg+ + m+a+r d  +ld+ +s yvdqwdwe  ++  +rnl +l e v++i+
  lcl|NCBI__GCF_000422285.1:WP_028322146.1 106 ATKWKRIALRQFGMQFGEGVLTDMRAVRKD-YFLDHDHSAYVDQWDWEMAITAEQRNLDFLTEVVRRIW 173
                                               ****************************98.59************************************ PP

                                 TIGR00669 142 aairatevavserfg.laal....lpkqivfvhseelvkrypdldskgredaiakelgavfligiggkl 205
                                               + ++ +e  v+  f  l++     lp++++f+h+e++++rypdl  k+re  i++e+ avf+ gig +l
  lcl|NCBI__GCF_000422285.1:WP_028322146.1 174 TVLKGAEQHVQSLFPaLKSSrypdLPDELTFIHAEDILERYPDLPRKQRETRIVQEYPAVFIYGIGWVL 242
                                               ************9952443223339******************************************** PP

                                 TIGR00669 206 sdgkphdvrapdyddwtteselg....ykglngdilvwnpvlgkafelssmgirvdedalrlqlaltgd 270
                                                dg ph++ra dyddw+te+ +      +glngdilvwnpv ++  el+smgirv++++lr+ql ++g+
  lcl|NCBI__GCF_000422285.1:WP_028322146.1 243 EDGYPHEMRAADYDDWATETVSRdgrpMHGLNGDILVWNPVTKRRHELTSMGIRVNAETLRQQLEISGQ 311
                                               *****************986432113379**************************************** PP

                                 TIGR00669 271 edrlelewhqdllngklpqtigggigqsrlamlllqkkhigevqasvwpkevre 324
                                                d l++ +hq++l+ ++p++igggigqsr  mlllqk h+gev  svwpk ++e
  lcl|NCBI__GCF_000422285.1:WP_028322146.1 312 LDLLKMPYHQAVLKNEIPLSIGGGIGQSRTFMLLLQKAHLGEVSVSVWPKVLKE 365
                                               **************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (376 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: 9.93
//
[ok]

This GapMind analysis is from Apr 10 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