Alignments for a candidate for asnA in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnA in Bacteroides thetaiotaomicron VPI-5482

Align aspartate-ammonia ligase (EC 6.3.1.1) (characterized)
to candidate 351657 BT2129 aspartate--ammonia ligase (NCBI ptt file)

Query= BRENDA::Q57WT9
         (351 letters)



>FitnessBrowser__Btheta:351657
          Length = 345

 Score =  323 bits (827), Expect = 5e-93
 Identities = 162/333 (48%), Positives = 221/333 (66%), Gaps = 20/333 (6%)

Query: 16  ILTVKRSFSEALEKELNLVEVRAPILFRVGDGTQDNLSGFEKAVQVPVKAIPNASFEVVH 75
           I  +K  F   L  EL L  V AP+    G G  D+L+G E+ V  P+K + +A  EVVH
Sbjct: 23  IKQIKEFFQLNLSSELRLRRVTAPLFVLKGMGINDDLNGIERPVSFPIKDLGDAQAEVVH 82

Query: 76  SLAKWKRRTLANYKFAPGHGLYTHMTALRVDDVLDNIHSVVVDQWDWEMVMKDDQRNLAF 135
           SLAKWKR TLA+Y   PG+G+YT M A+R D+ L N+HS+ VDQWDWE V+ ++ RN+ F
Sbjct: 83  SLAKWKRLTLADYNIEPGYGIYTDMNAIRSDEELGNLHSLYVDQWDWERVITNEDRNVEF 142

Query: 136 LKEVVCKVYAAIRKTELAVCEKYKQ-KPILPETIQFVHAEHLLLAYPNLTAKEREREIAR 194
           LKE+V ++YAA+ +TE  V E Y Q KP LP+ + F+H+E L   YPNL  K RE  I +
Sbjct: 143 LKEIVNRIYAAMIRTEYMVYEMYPQIKPCLPQKLHFIHSEELRQLYPNLEPKCREHAICQ 202

Query: 195 EYGAVFLIGIGAVLSSGDRHDARAPDYDDWTSPVEASQVVFPRTSKPIPTMNSLSSLKGL 254
           +YGAVF+IGIG  LS G +HD RAPDYDD+TS                     L++L GL
Sbjct: 203 KYGAVFIIGIGCKLSDGKKHDGRAPDYDDYTS-------------------TGLNNLPGL 243

Query: 255 NGDILLYNPTLDDSLEVSSMGIRVNAEALRHQISLTGDDSLLKSEWHQQLLNGEFPQTVG 314
           NGD+LL++  L  S+E+SSMG+RV+ EAL+ Q+    ++  LK  +H++L++   P ++G
Sbjct: 244 NGDLLLWDDVLQRSIELSSMGVRVDREALQRQLKEENEEERLKLYFHKRLMDDTLPLSIG 303

Query: 315 GGIGQSRMVMFMLRKKHIGEVQCSVWPEEIRKK 347
           GGIGQSR+ MF LRK HIGE+Q S+WPE++RK+
Sbjct: 304 GGIGQSRLCMFYLRKAHIGEIQASIWPEDMRKE 336


Lambda     K      H
   0.319    0.135    0.397 

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: 366
Number of extensions: 14
Number of successful extensions: 3
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: 351
Length of database: 345
Length adjustment: 29
Effective length of query: 322
Effective length of database: 316
Effective search space:   101752
Effective search space used:   101752
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 351657 BT2129 (aspartate--ammonia ligase (NCBI ptt file))
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.27572.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-120  389.0   0.0   1.2e-120  388.7   0.0    1.0  1  lcl|FitnessBrowser__Btheta:351657  BT2129 aspartate--ammonia ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351657  BT2129 aspartate--ammonia ligase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.7   0.0  1.2e-120  1.2e-120      11     328 ..      22     339 ..      13     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 388.7 bits;  conditional E-value: 1.2e-120
                          TIGR00669  11 eisfvkstftqklierlglievqgpilsqvgdgiqdnlsgiekavqvkvkaipdaafevvhslakwkrhtlarydf 86 
                                        +i  +k+ f  +l  +l l  v +p++   g gi+d+l gie+ v+  +k + da+ evvhslakwkr tla y++
  lcl|FitnessBrowser__Btheta:351657  22 GIKQIKEFFQLNLSSELRLRRVTAPLFVLKGMGINDDLNGIERPVSFPIKDLGDAQAEVVHSLAKWKRLTLADYNI 97 
                                        47789*********************************************************************** PP

                          TIGR00669  87 kedeglfvhmkalrpdedsldpvrsvyvdqwdwekvvpegernlaylketveaiyaairatevavserf.glaall 161
                                        + + g+++ m a+r de+ l +++s+yvdqwdwe+v+++ +rn+ +lke v++iyaa+  te +v e + ++++ l
  lcl|FitnessBrowser__Btheta:351657  98 EPGYGIYTDMNAIRSDEE-LGNLHSLYVDQWDWERVITNEDRNVEFLKEIVNRIYAAMIRTEYMVYEMYpQIKPCL 172
                                        ****************96.899*******************************************9998679**** PP

                          TIGR00669 162 pkqivfvhseelvkrypdldskgredaiakelgavfligiggklsdgkphdvrapdyddwtteselgykglngdil 237
                                        p++++f+hseel + yp+l+ k re+ai++++gavf+igig klsdgk+hd+rapdydd+t+   ++  glngd+l
  lcl|FitnessBrowser__Btheta:351657 173 PQKLHFIHSEELRQLYPNLEPKCREHAICQKYGAVFIIGIGCKLSDGKKHDGRAPDYDDYTSTGLNNLPGLNGDLL 248
                                        **************************************************************************** PP

                          TIGR00669 238 vwnpvlgkafelssmgirvdedalrlqlaltgdedrlelewhqdllngklpqtigggigqsrlamlllqkkhigev 313
                                        +w++vl++++elssmg+rvd +al++ql    +e+rl+l +h+ l++  lp++igggigqsrl+m+ l+k hige+
  lcl|FitnessBrowser__Btheta:351657 249 LWDDVLQRSIELSSMGVRVDREALQRQLKEENEEERLKLYFHKRLMDDTLPLSIGGGIGQSRLCMFYLRKAHIGEI 324
                                        **************************************************************************** PP

                          TIGR00669 314 qasvwpkevreeven 328
                                        qas+wp+++r+e e+
  lcl|FitnessBrowser__Btheta:351657 325 QASIWPEDMRKECEE 339
                                        **********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (345 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.96
//
[ok]

This GapMind analysis is from Apr 09 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