Alignments for a candidate for gatB in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Acidimicrobium ferrooxidans DSM 10331

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (uncharacterized)
to candidate WP_015798950.1 AFER_RS08030 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= curated2:Q2RGY5
         (476 letters)



>NCBI__GCF_000023265.1:WP_015798950.1
          Length = 483

 Score =  362 bits (928), Expect = e-104
 Identities = 217/488 (44%), Positives = 287/488 (58%), Gaps = 37/488 (7%)

Query: 3   YEAVIGLEVHAELKTASKAFCSCSTAFGGEPNTHVCPVCLGLPGVLPVINRQVVEFGLKT 62
           +E VIGLEVH EL+TA+K FC C+ AFG  PNT+VCPVCLGLPG LPV+N + VE  +  
Sbjct: 10  FELVIGLEVHVELRTATKLFCGCANAFGQAPNTNVCPVCLGLPGSLPVVNARCVEIAMAV 69

Query: 63  ALALNCRVAPFCKFDRKNYYYPDLPKNYQISQYDLPLATGGYLKINVDGQERVIGITRVH 122
             AL  RV    +F RKNY+YPD+PKNYQISQYD+P+  GG   + +DG  R I I R H
Sbjct: 70  GAALGSRVQS-SQFHRKNYFYPDMPKNYQISQYDVPICAGG--AVELDGGRR-IRIERAH 125

Query: 123 MEEDAGKLVHVDGPG----GGYSLVDYNRTGVPLLEIVSEPDLRSPAEARAYMEKLRAIL 178
           +EED GKL HV G G       +L+DYNR GVPLLEIVS PDLR P E RAY+ +LRAI+
Sbjct: 126 LEEDTGKLTHVGGGGRIESAERTLIDYNRAGVPLLEIVSAPDLRDPDEVRAYVSELRAIV 185

Query: 179 QYLDVSDCKMEEGSLRCDANVSVRPRGSQTFGTKTEVKNMNSFRALQRALEYEIERQIAI 238
             +  SD +MEEGSLR DANVSVRP GS+   T+ E+KN+NS R+LQRA+  E  RQI  
Sbjct: 186 VAVGASDGRMEEGSLRVDANVSVRPIGSEELRTRVELKNLNSLRSLQRAIAAEAMRQIES 245

Query: 239 LEGGGRVEQATMAWDESRGVTTVMRTKEQAHDYRYFPEPDLVPLEIDAAWIERVRREL-P 297
            E G  V Q T  WDE+RG T  +RTKE A DYRYFPEPDL PL +D A +E +   L  
Sbjct: 246 YERGEPVVQQTRHWDEARGATVGLRTKEAAEDYRYFPEPDLPPLVVDQAAVEAMSDLLVA 305

Query: 298 ELPDARCRRLMDTFGLPAYDAGVITSSRDLADYFDRVVARYPDAKVVSNWIMGDFLRLLN 357
            LP  R  RL D    P  D      S +L  Y    +     A +V+  +  +  + + 
Sbjct: 306 SLPRTRRARLADAAVSP--DVRETAVSEELWAYTRVALDAGLPATLVARRVANEIAQ-VR 362

Query: 358 ARNLEPGQAPVPPEELADLLELQKEGTISGKIAKQVL----------EEMFASGKGARQI 407
           ++ +E     + P  + ++L+ + +G +  +  ++VL          E + A+  G R+ 
Sbjct: 363 SQGVE-----IDPARVVEVLKAEADGLLLAQQVREVLRIAAERSDPIEALVAAVAGGREG 417

Query: 408 VQERGLVQISDTAALGKIVDEVLAANPNVVEDYRNGKEKALGFLVGQVMKATGGKANPGL 467
           ++          A   ++ +EV A+ P     +  G  K  GFLVGQV++ +GGK    L
Sbjct: 418 LE----------AEAARLAEEVAASAPEEWGRFVAGDAKIAGFLVGQVVRRSGGKVPGQL 467

Query: 468 VNKLLKER 475
             + L ER
Sbjct: 468 ARRALDER 475


Lambda     K      H
   0.318    0.137    0.401 

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: 637
Number of extensions: 24
Number of successful extensions: 5
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: 483
Length adjustment: 34
Effective length of query: 442
Effective length of database: 449
Effective search space:   198458
Effective search space used:   198458
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: 51 (24.3 bits)

Align candidate WP_015798950.1 AFER_RS08030 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
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.179106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-133  430.4   0.0   4.3e-133  430.2   0.0    1.0  1  NCBI__GCF_000023265.1:WP_015798950.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023265.1:WP_015798950.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.2   0.0  4.3e-133  4.3e-133       4     478 ..      10     474 ..       7     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 430.2 bits;  conditional E-value: 4.3e-133
                             TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 
                                           +elviGlEvHv l t++KlFc c n + +  pNtnvcpvclglPG+lPv+N + v+ A+ ++ al+s+++   
  NCBI__GCF_000023265.1:WP_015798950.1  10 FELVIGLEVHVELRTATKLFCGCANAFGQ-APNTNVCPVCLGLPGSLPVVNARCVEIAMAVGAALGSRVQ--S 79 
                                           89**************************9.9*************************************66..6 PP

                             TIGR00133  77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk....dkqsl 145
                                           s+F+RK+YfYpD+Pk+yqi+q+d+Pi+ +G +e++     ++i+ier hlEeDtgk+++ +       ++ +l
  NCBI__GCF_000023265.1:WP_015798950.1  80 SQFHRKNYFYPDMPKNYQISQYDVPICAGGAVELDGG---RRIRIERAHLEEDTGKLTHVGGGGriesAERTL 149
                                           ******************************8887655...59*****************976533556899** PP

                             TIGR00133 146 vDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEi 218
                                           +D+NR+gvPLlEiV++Pdl++++e+ra++++lr+i+  ++ sdg +eeGs+RvD+Nvs+r+ G+e+  trvE+
  NCBI__GCF_000023265.1:WP_015798950.1 150 IDYNRAGVPLLEIVSAPDLRDPDEVRAYVSELRAIVVAVGASDGRMEEGSLRVDANVSVRPIGSEELRTRVEL 222
                                           ************************************************************************* PP

                             TIGR00133 219 KNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideev 291
                                           KNlnsl+s+++ai  E +Rq++  ++ge v+q+tr++de++  tv lR Ke +eDYRYfpePdlpp+++d+  
  NCBI__GCF_000023265.1:WP_015798950.1 223 KNLNSLRSLQRAIAAEAMRQIESYERGEPVVQQTRHWDEARGATVGLRTKEAAEDYRYFPEPDLPPLVVDQAA 295
                                           ************************************************************************* PP

                             TIGR00133 292 vkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkk 364
                                           v+ +    +  lP+++r+rl  ++ +s +  ++ vs++ l  + + +  +  ++ l+++ + +e+++      
  NCBI__GCF_000023265.1:WP_015798950.1 296 VEAMSDLLVASLPRTRRARLA-DAAVSPDVRETAVSEE-LWAYTRVALDAGLPATLVARRVANEIAQ------ 360
                                           ***9999**********9986.6789999999999876.4444455555555556777777777653...... PP

                             TIGR00133 365 islaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveeviken 437
                                           +  + + ++p  ++e++k   +g + +++++e+l+   e+   +++l+ +        e e  ++ eev +  
  NCBI__GCF_000023265.1:WP_015798950.1 361 VRSQGVEIDPARVVEVLKAEADGLLLAQQVREVLRIAAERSDPIEALVAAVAGGREGLEAEAARLAEEVAASA 433
                                           344567899*****************************************888888888899*********** PP

                             TIGR00133 438 pkevekyksgkekalkflvGqvmkktkgradpkevekllke 478
                                           p+e  ++ +g  k+ +flvGqv++++ g++  + + + l+e
  NCBI__GCF_000023265.1:WP_015798950.1 434 PEEWGRFVAGDAKIAGFLVGQVVRRSGGKVPGQLARRALDE 474
                                           *****************************999888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (483 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: 16.57
//
[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