Alignments for a candidate for gatB in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Clostridium acetobutylicum ATCC 824

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate NP_349578.1 CA_C2976 aspartyl/glutamyl-tRNA amidotransferase subunit B

Query= metacyc::MONOMER-13956
         (476 letters)



>NCBI__GCF_000008765.1:NP_349578.1
          Length = 478

 Score =  483 bits (1244), Expect = e-141
 Identities = 236/472 (50%), Positives = 337/472 (71%), Gaps = 3/472 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M++ETVIGLEVH EL TK+KIF +  T FGA+ N  T  I +G PG LPVLN+E V  A+
Sbjct: 1   MSYETVIGLEVHAELSTKTKIFCNCSTKFGAKPNENTCPICMGLPGTLPVLNEEVVHLAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120
           KA  AL+C+I    K DRKNYFYPD PKAYQISQFD PI   G++EI      K++ + R
Sbjct: 61  KAGEALHCKINKLNKMDRKNYFYPDLPKAYQISQFDIPICSGGYVEIPTKDGVKKVRLNR 120

Query: 121 LHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
           +H+EEDAGKL H   + +SL+D+NR G PLVEIVSEPD+R+PEEA  +++ L++++QY  
Sbjct: 121 IHIEEDAGKLVHLEYEPHSLIDYNRVGVPLVEIVSEPDMRSPEEAVEFMKTLRAMLQYAN 180

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQV--LL 237
           +SDC+M++GS+RCDANISLR +G  E+ TK E+KN+NSF  +QK LE EEKRQ+++    
Sbjct: 181 ISDCRMDQGSMRCDANISLREVGSTEYNTKVEIKNINSFRELQKALEKEEKRQKELYDFN 240

Query: 238 SGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELP 297
            GF I+QETRR+D    KT+ MR KE ++DYRYFPEPD++ + + DE  E+VK  +PELP
Sbjct: 241 EGFRIKQETRRWDSGKGKTVTMRTKEDANDYRYFPEPDIIPIVVKDELLEKVKEEMPELP 300

Query: 298 DERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQ 357
            ER+ R+ ++    + +  +L   K +AD+FE+ V+ G E+K ASNW++G++   +   +
Sbjct: 301 VERKARFEDQYKLGSKEIEILIEDKALADYFEKLVEAGCESKTASNWILGDMLRLMRETE 360

Query: 358 KELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEG 417
            +   + +  E +  +I++I+   IS+  AK+VF+E+ +   + + +VKEKGL QISDE 
Sbjct: 361 TDSKAIPVPVEHMNQLIEMIKTKEISNTAAKEVFEEMFKTSKEPKVVVKEKGLSQISDES 420

Query: 418 VLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
            L K+V + ++NN +S+ D+K GK +AIG+LVGQ+MK SKG+ANPPMV ++L
Sbjct: 421 ALQKMVEDVINNNEKSVLDYKAGKKQAIGYLVGQVMKQSKGKANPPMVKELL 472


Lambda     K      H
   0.314    0.134    0.373 

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: 695
Number of extensions: 31
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: 476
Length of database: 478
Length adjustment: 33
Effective length of query: 443
Effective length of database: 445
Effective search space:   197135
Effective search space used:   197135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate NP_349578.1 CA_C2976 (aspartyl/glutamyl-tRNA amidotransferase subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

# 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.671.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   9.3e-183  594.0   9.0     1e-182  593.9   9.0    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349578.1  CA_C2976 aspartyl/glutamyl-tRNA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349578.1  CA_C2976 aspartyl/glutamyl-tRNA amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  593.9   9.0    1e-182    1e-182       2     480 ..       1     476 [.       1     477 [. 0.98

  Alignments for each domain:
  == domain 1  score: 593.9 bits;  conditional E-value: 1e-182
                              TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskiv 73 
                                            ++ye viGlEvH  l tk+K+Fc+cs+++   kpN+n+cp+c+glPG+lPvlN+e+v+ A+k ++al++ki+
  lcl|NCBI__GCF_000008765.1:NP_349578.1   1 MSYETVIGLEVHAELSTKTKIFCNCSTKFGA-KPNENTCPICMGLPGTLPVLNEEVVHLAVKAGEALHCKIN 71 
                                            579**************************99.**************************************66 PP

                              TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqsl 145
                                             +  + dRK+YfYpDlPk+yqi+q+d+Pi+++G++ei ++++ k+++++r+h+EeD+gk+++ e +   +sl
  lcl|NCBI__GCF_000008765.1:NP_349578.1  72 -KLNKMDRKNYFYPDLPKAYQISQFDIPICSGGYVEIPTKDGVKKVRLNRIHIEEDAGKLVHLEYE--PHSL 140
                                            .6*************************************************************775..7*** PP

                              TIGR00133 146 vDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvE 217
                                            +D+NR gvPL+EiV++Pd++s++ea++f+k lr++l+y +isd+ +++GsmR+D+N+s+r +G+++  t+vE
  lcl|NCBI__GCF_000008765.1:NP_349578.1 141 IDYNRVGVPLVEIVSEPDMRSPEEAVEFMKTLRAMLQYANISDCRMDQGSMRCDANISLREVGSTEYNTKVE 212
                                            ************************************************************************ PP

                              TIGR00133 218 iKNlnslksiekaieyEieRqkkll..kkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppiei 287
                                            iKN+ns+++++ka+e E +Rqk+l   ++g  +kqetr +d  k +tv++R Ke+++DYRYfpePd+ pi++
  lcl|NCBI__GCF_000008765.1:NP_349578.1 213 IKNINSFRELQKALEKEEKRQKELYdfNEGFRIKQETRRWDSGKGKTVTMRTKEDANDYRYFPEPDIIPIVV 284
                                            ***********************96226889***************************************** PP

                              TIGR00133 288 deevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellge 359
                                            ++e++++ v+e++pelP ++++r++ +y+l +++ ++l++d+ l+d+fe++v++  e+k+a nWil ++l+ 
  lcl|NCBI__GCF_000008765.1:NP_349578.1 285 KDELLEK-VKEEMPELPVERKARFEDQYKLGSKEIEILIEDKALADYFEKLVEAGCESKTASNWILGDMLRL 355
                                            ****999.**************************************************************** PP

                              TIGR00133 360 Lnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkive 431
                                            +++++++ ++  +  e++ +li++ik ++is+++ake++ee++++ k+pk +++++gl+qisde++l+k+ve
  lcl|NCBI__GCF_000008765.1:NP_349578.1 356 MRETETDSKAIPVPVEHMNQLIEMIKTKEISNTAAKEVFEEMFKTSKEPKVVVKEKGLSQISDESALQKMVE 427
                                            ************************************************************************ PP

                              TIGR00133 432 evikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                            +vi++n+k+v++yk+gk++a+++lvGqvmk++kg+a+p  v++ll+++l
  lcl|NCBI__GCF_000008765.1:NP_349578.1 428 DVINNNEKSVLDYKAGKKQAIGYLVGQVMKQSKGKANPPMVKELLEKVL 476
                                            **********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.03
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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