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.1403735.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.53
//
[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:

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:

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:

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:

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