Alignments for a candidate for asnA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnA in Klebsiella michiganensis M5al

Align Aspartate--ammonia ligase; Asparagine synthetase A; EC 6.3.1.1 (characterized)
to candidate BWI76_RS00250 BWI76_RS00250 asparagine synthetase A

Query= SwissProt::P00963
         (330 letters)



>FitnessBrowser__Koxy:BWI76_RS00250
          Length = 330

 Score =  602 bits (1552), Expect = e-177
 Identities = 296/330 (89%), Positives = 312/330 (94%)

Query: 1   MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK 60
           MKTAYIAKQRQISFVKSHFSRQLEE+LGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK
Sbjct: 1   MKTAYIAKQRQISFVKSHFSRQLEEKLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK 60

Query: 61  ALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWE 120
            LPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRL+ +HSVYVDQWDWE
Sbjct: 61  TLPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLTAIHSVYVDQWDWE 120

Query: 121 RVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDL 180
           RVMGD ER   TLK+TVEAI+AGIKATE AVS+EFGL PFLP+ IHFVHSQELLSRYPDL
Sbjct: 121 RVMGDEERHCGTLKATVEAIYAGIKATEDAVSKEFGLTPFLPETIHFVHSQELLSRYPDL 180

Query: 181 DAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWN 240
           DAKGRERAIAK+LGAVFL+GIGGKLSDG RHDVRAPDYDDWSTP+  G+AGLNGDILVWN
Sbjct: 181 DAKGRERAIAKELGAVFLIGIGGKLSDGQRHDVRAPDYDDWSTPAAEGYAGLNGDILVWN 240

Query: 241 PVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRL 300
           PVLEDAFELSSMGIRVDA+ LK QLA+TGDEDRL+LEWHQALLRGEMPQTIGGGIGQSRL
Sbjct: 241 PVLEDAFELSSMGIRVDAEALKRQLAMTGDEDRLKLEWHQALLRGEMPQTIGGGIGQSRL 300

Query: 301 TMLLLQLPHIGQVQCGVWPAAVRESVPSLL 330
           TMLLLQL HIGQVQCGVWP  VR+SV +LL
Sbjct: 301 TMLLLQLDHIGQVQCGVWPTQVRQSVAALL 330


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: 552
Number of extensions: 7
Number of successful extensions: 1
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: 330
Length adjustment: 28
Effective length of query: 302
Effective length of database: 302
Effective search space:    91204
Effective search space used:    91204
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 BWI76_RS00250 BWI76_RS00250 (asparagine synthetase A)
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.12332.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.4e-195  632.8   0.2   7.2e-195  632.7   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00250  BWI76_RS00250 asparagine synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00250  BWI76_RS00250 asparagine synthetase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.7   0.2  7.2e-195  7.2e-195       1     330 []       1     330 []       1     330 [] 1.00

  Alignments for each domain:
  == domain 1  score: 632.7 bits;  conditional E-value: 7.2e-195
                               TIGR00669   1 mkkafilkqqeisfvkstftqklierlglievqgpilsqvgdgiqdnlsgiekavqvkvkaipdaafevvh 71 
                                             mk+a+i+kq++isfvks+f+++l+e+lglievq+pils+vgdg+qdnlsg+ekavqvkvk++pda+fevvh
  lcl|FitnessBrowser__Koxy:BWI76_RS00250   1 MKTAYIAKQRQISFVKSHFSRQLEEKLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVKTLPDAQFEVVH 71 
                                             9********************************************************************** PP

                               TIGR00669  72 slakwkrhtlarydfkedeglfvhmkalrpdedsldpvrsvyvdqwdwekvvpegernlaylketveaiya 142
                                             slakwkr+tl+++df+++egl++hmkalrpded+l  ++svyvdqwdwe+v+++ er+  +lk tveaiya
  lcl|FitnessBrowser__Koxy:BWI76_RS00250  72 SLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLTAIHSVYVDQWDWERVMGDEERHCGTLKATVEAIYA 142
                                             *********************************************************************** PP

                               TIGR00669 143 airatevavserfglaallpkqivfvhseelvkrypdldskgredaiakelgavfligiggklsdgkphdv 213
                                             +i+ate avs++fgl+++lp+ i+fvhs+el++rypdld+kgre+aiakelgavfligiggklsdg++hdv
  lcl|FitnessBrowser__Koxy:BWI76_RS00250 143 GIKATEDAVSKEFGLTPFLPETIHFVHSQELLSRYPDLDAKGRERAIAKELGAVFLIGIGGKLSDGQRHDV 213
                                             *********************************************************************** PP

                               TIGR00669 214 rapdyddwtteselgykglngdilvwnpvlgkafelssmgirvdedalrlqlaltgdedrlelewhqdlln 284
                                             rapdyddw+t++ +gy+glngdilvwnpvl++afelssmgirvd++al++qla+tgdedrl+lewhq+ll+
  lcl|FitnessBrowser__Koxy:BWI76_RS00250 214 RAPDYDDWSTPAAEGYAGLNGDILVWNPVLEDAFELSSMGIRVDAEALKRQLAMTGDEDRLKLEWHQALLR 284
                                             *********************************************************************** PP

                               TIGR00669 285 gklpqtigggigqsrlamlllqkkhigevqasvwpkevreevenil 330
                                             g++pqtigggigqsrl+mlllq +hig+vq++vwp +vr++v ++l
  lcl|FitnessBrowser__Koxy:BWI76_RS00250 285 GEMPQTIGGGIGQSRLTMLLLQLDHIGQVQCGVWPTQVRQSVAALL 330
                                             *****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (330 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: 00:00:00.01
# Mc/sec: 7.00
//
[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