Alignments for a candidate for gatB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Caulobacter crescentus NA1000

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate CCNA_02518 CCNA_02518 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Caulo:CCNA_02518
          Length = 498

 Score =  425 bits (1092), Expect = e-123
 Identities = 221/483 (45%), Positives = 328/483 (67%), Gaps = 15/483 (3%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E V+GLEVH ++ + SK+FS +   FGA PN   +++D A PG+LPV+N+  V+ A++ 
Sbjct: 15  WEMVLGLEVHAQVASKSKLFSGAAVGFGAGPNEQVSLVDAAMPGMLPVLNRFCVEQAVKT 74

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVD-GETKRIGITRL 121
            + L  +I  +S+FDRKNYFYPD P+ YQISQFDQPI   G + +E D G T  + I RL
Sbjct: 75  GLGLRAQINLKSRFDRKNYFYPDLPQGYQISQFDQPIVGEGVVSVERDDGTTFDVRIERL 134

Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+E+DAGKS H  +   + VDLNR GT L+EIVS+PD+R+ +EA AY++KLR+I+ Y G 
Sbjct: 135 HLEQDAGKSLHDQDPNATYVDLNRAGTALMEIVSKPDMRTSEEAAAYVKKLRTILVYLGT 194

Query: 180 SDVKMEEGSLRCDANISL-RPYGQEKF---------GTKAELKNLNSFNYVRKGLEYEEK 229
            D  ME+G+LR D N+S+ RP   EKF         GT+ E+KN+NS+ Y+++ +EYE +
Sbjct: 195 CDGDMEKGNLRADVNVSVCRPGDYEKFRATGDFKHLGTRCEIKNVNSYRYIQQAIEYEAR 254

Query: 230 RQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVR 289
           RQ E L  GG++ QETR FD + G+T  MR KE + DYRYFP+PD++PL +D AW + + 
Sbjct: 255 RQIEILEDGGKVDQETRLFDPTKGETRSMRSKEEAHDYRYFPDPDLLPLVLDPAWVKSIE 314

Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349
           +T+PELPD +KA+  ++ GL AYDA VL +  + +D+FE+  + G D KL +NW+   + 
Sbjct: 315 ETLPELPDAKKARLQSQYGLSAYDAGVLIIDADRADYFEAAAK-GRDAKLVANWVTNELL 373

Query: 350 EYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGL 409
             L+    E  ++ L   ++A +++LIE+GT+SSKIAK+VF  + A  G   +I+E  GL
Sbjct: 374 AKLSAAGTEFTNSPLPHTDIAQLVELIENGTISSKIAKEVFEHMWAGEGRPAEIVEKRGL 433

Query: 410 VQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLK 469
           VQI+D   + K +++ +  N    E  K+ K +A+G+ VGQ+MKA+ G+ANP  VN+LL+
Sbjct: 434 VQINDTGAIEKAIDDLIAGNPDKAEAVKD-KPQALGWFVGQVMKATGGKANPGTVNELLR 492

Query: 470 QEL 472
           ++L
Sbjct: 493 KKL 495


Lambda     K      H
   0.313    0.133    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: 646
Number of extensions: 32
Number of successful extensions: 6
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: 475
Length of database: 498
Length adjustment: 34
Effective length of query: 441
Effective length of database: 464
Effective search space:   204624
Effective search space used:   204624
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: 52 (24.6 bits)

Align candidate CCNA_02518 CCNA_02518 (aspartyl/glutamyl-tRNA(Asn/Gln) 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.7868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-162  525.7   0.0   5.6e-162  525.5   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02518  CCNA_02518 aspartyl/glutamyl-tRN


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02518  CCNA_02518 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.5   0.0  5.6e-162  5.6e-162       3     480 ..      14     495 ..      12     496 .. 0.95

  Alignments for each domain:
  == domain 1  score: 525.5 bits;  conditional E-value: 5.6e-162
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           ++e+v+GlEvH q+  ksKlF+ +   +    pN++v+ v+ ++PG lPvlN+  v++A+k +l l ++i+  
  lcl|FitnessBrowser__Caulo:CCNA_02518  14 DWEMVLGLEVHAQVASKSKLFSGAAVGFGA-GPNEQVSLVDAAMPGMLPVLNRFCVEQAVKTGLGLRAQIN-L 84 
                                           679*************************99.9*************************************77.5 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvD 147
                                           +s FdRK+YfYpDlP+gyqi+q+d+Pi+ +G++++e +++    ++ierlhlE+D+gks + ++  ++ ++vD
  lcl|FitnessBrowser__Caulo:CCNA_02518  85 KSRFDRKNYFYPDLPQGYQISQFDQPIVGEGVVSVERDDGTtFDVRIERLHLEQDAGKSLHDQD--PNATYVD 155
                                           9***********************************99877479*****************966..79***** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq..........e 210
                                           +NR+g+ L+EiV+kPd+++++ea+a++kklr+il yl+  dgd+e+G++R+DvNvs+   G+          +
  lcl|FitnessBrowser__Caulo:CCNA_02518 156 LNRAGTALMEIVSKPDMRTSEEAAAYVKKLRTILVYLGTCDGDMEKGNLRADVNVSVCRPGDyekfratgdfK 228
                                           *********************************************************7654422222222246 PP

                             TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlp 283
                                           + gtr EiKN+ns + i++aieyE  Rq+++l++g +v qetr fd +k  t s+R+Kee++DYRYfp+Pdl 
  lcl|FitnessBrowser__Caulo:CCNA_02518 229 HLGTRCEIKNVNSYRYIQQAIEYEARRQIEILEDGGKVDQETRLFDPTKGETRSMRSKEEAHDYRYFPDPDLL 301
                                           789********************************************************************** PP

                             TIGR00133 284 pieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileel 356
                                           p+++d+ +vk+ +ee+lpelP+ak++rl+++ygls++da vl+ d++ +d+fe ++k  +  kl++nW+++el
  lcl|FitnessBrowser__Caulo:CCNA_02518 302 PLVLDPAWVKS-IEETLPELPDAKKARLQSQYGLSAYDAGVLIIDADRADYFEAAAKGRDA-KLVANWVTNEL 372
                                           **********9.****************************************999887666.*********** PP

                             TIGR00133 357 lgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvki 429
                                           l++L +  ++++++ l  +++a+l++li++g+is+k+ake++e++   ++ p +++ek+gl+qi+d+ ++ k+
  lcl|FitnessBrowser__Caulo:CCNA_02518 373 LAKLSAAGTEFTNSPLPHTDIAQLVELIENGTISSKIAKEVFEHMWAGEGRPAEIVEKRGLVQINDTGAIEKA 445
                                           ************************************************************************* PP

                             TIGR00133 430 veevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +++ i+ np++ e  k+ k +al+++vGqvmk t g+a+p +v++ll+++l
  lcl|FitnessBrowser__Caulo:CCNA_02518 446 IDDLIAGNPDKAEAVKD-KPQALGWFVGQVMKATGGKANPGTVNELLRKKL 495
                                           ***********998876.6789*************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (498 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: 7.66
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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