Alignments for a candidate for asnA in Roseburia faecis M72

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnA in Roseburia faecis M72

Align Aspartate--ammonia ligase; Asparagine synthetase A; EC 6.3.1.1 (characterized)
to candidate WP_022046005.1 M72_RS13405 aspartate--ammonia ligase

Query= SwissProt::P00963
         (330 letters)



>NCBI__GCF_001406815.1:WP_022046005.1
          Length = 336

 Score =  252 bits (643), Expect = 1e-71
 Identities = 139/312 (44%), Positives = 183/312 (58%), Gaps = 11/312 (3%)

Query: 9   QRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVKALPDAQFE 68
           Q  I  VK  F   L +RL L  V AP+      G  DNL+G E+ V   +K   D   E
Sbjct: 20  QLAIKTVKDFFQALLAQRLHLTRVSAPLFVDPATGLNDNLNGYERPVTFGIKEQDDKNAE 79

Query: 69  VVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGER 128
           VVHSLAKWKR  L ++ F  GEG+YT M A+R DE     +HS++VDQWDWE+++   +R
Sbjct: 80  VVHSLAKWKRYALKKYGFQVGEGIYTDMNAIRRDEST-DNIHSIFVDQWDWEKIIHKEDR 138

Query: 129 QFSTLKSTVEAIWAGIKATEAAVSEEFGLAPF-LPDQIHFVHSQELLSRYPDLDAKGRER 187
               LK TV  ++  ++ TE  ++ ++      LP +I F+ SQEL   +PD   K RE 
Sbjct: 139 NLDYLKETVRTVYKCLRKTEQYMAIQYDYIDLILPKEIFFITSQELEDLFPDNTPKEREY 198

Query: 188 AIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAF 247
            I K  GAV ++ IG  L  G  HD RAPDYDDW+         LN DILV+ PVL+ A 
Sbjct: 199 YITKAKGAVCIMQIGDTLESGEPHDGRAPDYDDWA---------LNADILVYYPVLDIAL 249

Query: 248 ELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQL 307
           ELSSMGIRVD   L  QL   G  +R +L + ++++ G +P TIGGGIGQSR+ M  L+ 
Sbjct: 250 ELSSMGIRVDKTALISQLDKAGCPERKDLPFQKSIIDGTLPYTIGGGIGQSRICMFFLRK 309

Query: 308 PHIGQVQCGVWP 319
            HIG+VQ  +WP
Sbjct: 310 AHIGEVQSSLWP 321


Lambda     K      H
   0.318    0.136    0.410 

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: 305
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: 330
Length of database: 336
Length adjustment: 28
Effective length of query: 302
Effective length of database: 308
Effective search space:    93016
Effective search space used:    93016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_022046005.1 M72_RS13405 (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.3095942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-102  327.5   0.0   6.7e-102  327.1   0.0    1.1  1  NCBI__GCF_001406815.1:WP_022046005.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001406815.1:WP_022046005.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.1   0.0  6.7e-102  6.7e-102       9     323 ..      20     325 ..      14     331 .. 0.97

  Alignments for each domain:
  == domain 1  score: 327.1 bits;  conditional E-value: 6.7e-102
                             TIGR00669   9 qqeisfvkstftqklierlglievqgpilsqvgdgiqdnlsgiekavqvkvkaipdaafevvhslakwkrhtl 81 
                                           q  i  vk+ f   l +rl l  v +p++     g++dnl g e+ v   +k   d + evvhslakwkr +l
  NCBI__GCF_001406815.1:WP_022046005.1  20 QLAIKTVKDFFQALLAQRLHLTRVSAPLFVDPATGLNDNLNGYERPVTFGIKEQDDKNAEVVHSLAKWKRYAL 92 
                                           667999******************************************************************* PP

                             TIGR00669  82 arydfkedeglfvhmkalrpdedsldpvrsvyvdqwdwekvvpegernlaylketveaiyaairatevavser 154
                                            +y+f+ +eg+++ m a+r de   d+++s++vdqwdwek++ + +rnl ylketv+++y+++r+te  +  +
  NCBI__GCF_001406815.1:WP_022046005.1  93 KKYGFQVGEGIYTDMNAIRRDES-TDNIHSIFVDQWDWEKIIHKEDRNLDYLKETVRTVYKCLRKTEQYMAIQ 164
                                           *********************95.69*********************************************** PP

                             TIGR00669 155 fg.laallpkqivfvhseelvkrypdldskgredaiakelgavfligiggklsdgkphdvrapdyddwttese 226
                                           ++ +  +lpk+i f+ s+el   +pd   k+re  i+k  gav ++ ig  l  g+phd+rapdyddw+    
  NCBI__GCF_001406815.1:WP_022046005.1 165 YDyIDLILPKEIFFITSQELEDLFPDNTPKEREYYITKAKGAVCIMQIGDTLESGEPHDGRAPDYDDWA---- 233
                                           9956789*************************************************************6.... PP

                             TIGR00669 227 lgykglngdilvwnpvlgkafelssmgirvdedalrlqlaltgdedrlelewhqdllngklpqtigggigqsr 299
                                                ln dilv+ pvl+ a+elssmgirvd++al  ql  +g  +r +l + +++++g lp tigggigqsr
  NCBI__GCF_001406815.1:WP_022046005.1 234 -----LNADILVYYPVLDIALELSSMGIRVDKTALISQLDKAGCPERKDLPFQKSIIDGTLPYTIGGGIGQSR 301
                                           .....9******************************************************************* PP

                             TIGR00669 300 lamlllqkkhigevqasvwpkevr 323
                                           ++m++l+k higevq+s+wp+e  
  NCBI__GCF_001406815.1:WP_022046005.1 302 ICMFFLRKAHIGEVQSSLWPEETI 325
                                           ********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (336 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: 17.60
//
[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