Alignments for a candidate for gatA in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Pseudomonas fluorescens FW300-N2E3

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate AO353_05260 AO353_05260 glutamyl-tRNA amidotransferase

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05260
          Length = 483

 Score =  496 bits (1276), Expect = e-145
 Identities = 246/480 (51%), Positives = 335/480 (69%), Gaps = 3/480 (0%)

Query: 6   HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63
           H++T  E+ + +  K+    +L      RI  +D ++ +F++L E+ A + AK  D    
Sbjct: 2   HQLTLAEIARGLADKKFSSEELTKVLLARIAQLDPQLNSFISLTEDLALSQAKAADVR-R 60

Query: 64  GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123
              E G L G PI  KD   T+G+RT+C SK+L+NF   YDATVV +L  A AVT+GK N
Sbjct: 61  ANGESGALLGAPIAHKDLFCTQGIRTSCGSKMLDNFKAPYDATVVAKLAAAGAVTLGKTN 120

Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183
           MDEFAMGS+ E+S Y   KNPWNL+ VPGGSSGGSAAAVAA  +P +  +DTGGSIRQPA
Sbjct: 121 MDEFAMGSANESSYYGAVKNPWNLEHVPGGSSGGSAAAVAARLLPAATATDTGGSIRQPA 180

Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243
           +F  + GLKPTYGRVSR+G++A+ASSLDQ GP+ RT ED A LLQ ++G D  DSTS + 
Sbjct: 181 AFTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCAILLQGMAGFDPKDSTSIDE 240

Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303
            VPD+ + L G ++GL+I VPKEY   G+     E +  ++K LE LGA  +E+SLP+ +
Sbjct: 241 PVPDYSAGLNGSLQGLRIGVPKEYFSAGLDPRIAELIHNSVKELEKLGAVVKEISLPNMQ 300

Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363
           +A+  YY+++ +EAS+NL+RFDG+R+GYR +N  +L DLYK++R EGFG EV+RRIM+G 
Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCENPKDLTDLYKRSRGEGFGPEVQRRIMVGA 360

Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYA 423
           +ALS+GYYDAYY KAQK+R L+K DF   F + D+I+GPTTP PA+K+G    DP+  Y 
Sbjct: 361 YALSAGYYDAYYLKAQKIRRLVKNDFMAAFNEVDIILGPTTPNPAWKLGAKNSDPVAAYL 420

Query: 424 NDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
            D+ TI  NLAG+PG+S+P G  DGLP+G+Q++  +F E  +  VAH ++  TD H   P
Sbjct: 421 EDVYTITANLAGLPGLSMPAGFVDGLPVGVQLLAPYFQEGRLLNVAHQYQLNTDWHTRTP 480


Lambda     K      H
   0.315    0.134    0.381 

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: 566
Number of extensions: 16
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: 485
Length of database: 483
Length adjustment: 34
Effective length of query: 451
Effective length of database: 449
Effective search space:   202499
Effective search space used:   202499
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate AO353_05260 AO353_05260 (glutamyl-tRNA amidotransferase)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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/TIGR00132.hmm
# target sequence database:        /tmp/gapView.19298.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   6.9e-181  588.0   0.0   7.8e-181  587.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260  AO353_05260 glutamyl-tRNA amidot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260  AO353_05260 glutamyl-tRNA amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.8   0.0  7.8e-181  7.8e-181       5     463 ..      13     472 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 587.8 bits;  conditional E-value: 7.8e-181
                                     TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKd 67 
                                                   l +k++s++e+++ +l+ri + + ++n+f+++t++ al++ak+ d + a  e   l g pia Kd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260  13 LADKKFSSEELTKVLLARIAQLDPQLNSFISLTEDLALSQAKAADVRRAnGEsGALLGAPIAHKD 77 
                                                   678999***************************************988865636*********** PP

                                     TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPe 132
                                                    +++++i+t+c+Sk+L+n+++pydatVv +l +aga+++GktN+DEFamGs+ e+S++g++knP+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260  78 LFCTQGIRTSCGSKMLDNFKAPYDATVVAKLAAAGAVTLGKTNMDEFAMGSANESSYYGAVKNPW 142
                                                   ***************************************************************** PP

                                     TIGR00132 133 neervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSl 197
                                                   n e+vpGGSsgGsaaavaa l p a ++DTGgSiRqPA+f++  GlKPtYG+vSR+G++ayasSl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260 143 NLEHVPGGSSGGSAAAVAARLLPAATATDTGGSIRQPAAFTNLTGLKPTYGRVSRWGMIAYASSL 207
                                                   ***************************************************************** PP

                                     TIGR00132 198 dqiGilakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldke 262
                                                   dq G+la++ ed a++l+ ++g D kDsts++ +v+++   l+  l+gl++gv ke++  +ld +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260 208 DQGGPLARTAEDCAILLQGMAGFDPKDSTSIDEPVPDYSAGLNGSLQGLRIGVPKEYFSAGLDPR 272
                                                   ***************************************************************** PP

                                     TIGR00132 263 vkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslk 327
                                                   ++e +++ +++le+lga ++e+slp+++ a+++Yy+i+p+Eassnl+r+dg+r+G+r e++k+l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260 273 IAELIHNSVKELEKLGAVVKEISLPNMQHAIPAYYVIAPAEASSNLSRFDGVRFGYRCENPKDLT 337
                                                   ***************************************************************** PP

                                     TIGR00132 328 elyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptap 392
                                                   +ly+++R egfg ev+rRim+Gayals++yyd+yy+kAqk+r+l++++f  +f+evD+i++pt+p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260 338 DLYKRSRGEGFGPEVQRRIMVGAYALSAGYYDAYYLKAQKIRRLVKNDFMAAFNEVDIILGPTTP 402
                                                   ***************************************************************** PP

                                     TIGR00132 393 tlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsva 457
                                                     a klg+k++dp++ yl+Dv+t++anlaGlp++s+P+g   +glp+G+q+ + +f++ +ll+va
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260 403 NPAWKLGAKNSDPVAAYLEDVYTITANLAGLPGLSMPAGFV-DGLPVGVQLLAPYFQEGRLLNVA 466
                                                   *****************************************.7********************** PP

                                     TIGR00132 458 kaleqa 463
                                                   ++++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05260 467 HQYQLN 472
                                                   *99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.17
//
[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