Alignments for a candidate for gatA in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Acidimicrobium ferrooxidans DSM 10331

Align Glutamyl-tRNA(Gln) amidotransferase subunit A, chloroplastic/mitochondrial; Glu-AdT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_015798951.1 AFER_RS08035 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::Q9LI77
         (537 letters)



>NCBI__GCF_000023265.1:WP_015798951.1
          Length = 479

 Score =  414 bits (1064), Expect = e-120
 Identities = 221/471 (46%), Positives = 310/471 (65%), Gaps = 13/471 (2%)

Query: 51  RSLLSGETTAVEIAKSYLSRIRLTEPQLKCFLHVS-ENVLKDAQEIDQRIAKGEELGPLA 109
           R++  G   A E+ ++Y +++ + EP++  FLH+  +   + A  +D  +  G + GPLA
Sbjct: 16  RAVREGAVRAEEVLEAYEAQVAVEEPEVHAFLHLDFDAARRRAAAVDAAVRAGHDPGPLA 75

Query: 110 GVLIGVKDNICTQGMPSTAASRILEHYRPPFDATAVKKIKELGGIVVGKTNMDEFGMGST 169
           GV I +KDNI  +G+P+TA SRILE +  P+ AT V ++   GG++VGKTN+DEF MGS+
Sbjct: 76  GVPIAIKDNIVQEGVPTTAGSRILEGWVSPYSATVVDRVLAAGGVIVGKTNLDEFAMGSS 135

Query: 170 TEASAFQVTANPWDLSRVPGGSSGGSAAAVAARQCMVSLGSDTGGSVRQPASFCGVVGLK 229
           TE SAF  T NP DL RVPGGSSGGSAAAVAAR   ++LGSDTGGS+RQPAS CGVVG+K
Sbjct: 136 TENSAFGPTRNPHDLDRVPGGSSGGSAAAVAARFSALALGSDTGGSIRQPASLCGVVGVK 195

Query: 230 PTYGRVSRFGLMAYASSLDVIGCFGSTVADAGMLLHAISGYDRFDSTSSKQDVPEFQSQF 289
           PTYG +SR+GL+A+ASSLD IG F +TV DA  LL  +SG+D  D+TS+ +         
Sbjct: 196 PTYGAISRYGLIAFASSLDQIGPFAATVDDAAALLAVLSGHDPRDATSAPRGP------- 248

Query: 290 LSVDHFESKPLNGVKVGIIRETLEDGVDSGVRSATQEAASHLEALGCILTEVSLPSFSLG 349
             V     + + G  VG++ E L +  D  V +A + AA HLE LG  +  VS+P  +  
Sbjct: 249 -IVSDPSDRDVAGWTVGVVTE-LAETADPAVAAALEAAARHLERLGASVVSVSIPEVAAA 306

Query: 350 LPAYYVIASSESSSNLSRYDGVRYGNQVMAEELNKLYECSRGEGFGGEVKMRILMGTYAL 409
           L AYYV+A +E+SSNL+R+DGVRYG +V A   +++   +R  GFG EVK RI++GTYAL
Sbjct: 307 LAAYYVVAPAEASSNLARFDGVRYGLRVEALTTDEMMVATRSAGFGDEVKRRIMLGTYAL 366

Query: 410 SAGYYDAYYKRAQQVRTLIRKDFKAALEQNDILISPAAPSAAYKIGEKKDDPLAMYAGDI 469
           SAGY DA Y +AQ+VRT +      A    D+LI+P +P+ A+++GE+  DP+AMY  D+
Sbjct: 367 SAGYRDALYVQAQRVRTWLAAGLARAFADVDVLITPTSPTTAFRLGERVADPVAMYRSDV 426

Query: 470 MTVNVNLAGLPAMVLPCGLVEGGPSGLPVGLQMIGAAFDEEKLLKVGHIFE 520
            TV  NL G PA+ +P G        LP+G+Q++  A+++ ++L      E
Sbjct: 427 CTVPSNLVGGPAVSVPFGY---DADRLPIGIQVMAPAWEDARMLVAARALE 474


Lambda     K      H
   0.316    0.133    0.375 

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: 583
Number of extensions: 31
Number of successful extensions: 4
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: 537
Length of database: 479
Length adjustment: 34
Effective length of query: 503
Effective length of database: 445
Effective search space:   223835
Effective search space used:   223835
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 WP_015798951.1 AFER_RS08035 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.22379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-175  570.7   0.0   1.4e-175  570.4   0.0    1.0  1  lcl|NCBI__GCF_000023265.1:WP_015798951.1  AFER_RS08035 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023265.1:WP_015798951.1  AFER_RS08035 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.4   0.0  1.4e-175  1.4e-175       4     462 ..      17     475 ..      14     478 .. 0.97

  Alignments for each domain:
  == domain 1  score: 570.4 bits;  conditional E-value: 1.4e-175
                                 TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdni 69 
                                               ++ +  v+++evle++++++   + +++afl+++ + a ++a+++d++v+  ++  +lag+pia+Kdni
  lcl|NCBI__GCF_000023265.1:WP_015798951.1  17 AVREGAVRAEEVLEAYEAQVAVEEPEVHAFLHLDFDAARRRAAAVDAAVRagHDpGPLAGVPIAIKDNI 85 
                                               566778999***************************************99854445************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138
                                               + ++++tt++S+iLe++vspy+atVv r+ +ag +i+GktNlDEFamGsste+Safg+t+nP++ +rvp
  lcl|NCBI__GCF_000023265.1:WP_015798951.1  86 VQEGVPTTAGSRILEGWVSPYSATVVDRVLAAGGVIVGKTNLDEFAMGSSTENSAFGPTRNPHDLDRVP 154
                                               ********************************************************************* PP

                                 TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207
                                               GGSsgGsaaavaa    lalgsDTGgSiRqPAs+cgvvG+KPtYG++SRyGl+a+asSldqiG++a++v
  lcl|NCBI__GCF_000023265.1:WP_015798951.1 155 GGSSGGSAAAVAARFSALALGSDTGGSIRQPASLCGVVGVKPTYGAISRYGLIAFASSLDQIGPFAATV 223
                                               ********************************************************************* PP

                                 TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276
                                               +d+a +l+v+sg+D +D ts+   +  +     +d+ g  vgvv el e+ +d +v++++e++ ++le+
  lcl|NCBI__GCF_000023265.1:WP_015798951.1 224 DDAAALLAVLSGHDPRDATSAPRGPI-VSDPSDRDVAGWTVGVVTELAET-ADPAVAAALEAAARHLER 290
                                               *********************99763.55555568**************9.****************** PP

                                 TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345
                                               lga +v vs+p+v  ala+Yy+++p+Eassnlar+dg+ryG rve l+  +e++++tRs+gfg+evkrR
  lcl|NCBI__GCF_000023265.1:WP_015798951.1 291 LGASVVSVSIPEVAAALAAYYVVAPAEASSNLARFDGVRYGLRVEALT-TDEMMVATRSAGFGDEVKRR 358
                                               ***********************************************9.9******************* PP

                                 TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414
                                               imlG+yals++y d+ y +Aq+vrt ++  +  +f +vDv+++pt+pt+af+lge+ +dp++my sDv+
  lcl|NCBI__GCF_000023265.1:WP_015798951.1 359 IMLGTYALSAGYRDALYVQAQRVRTWLAAGLARAFADVDVLITPTSPTTAFRLGERVADPVAMYRSDVC 427
                                               ********************************************************************* PP

                                 TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleq 462
                                               tvp nl+G pa+svP+g + + lpiG+q+++ a++d ++l +a+ale+
  lcl|NCBI__GCF_000023265.1:WP_015798951.1 428 TVPSNLVGGPAVSVPFGYDADRLPIGIQVMAPAWEDARMLVAARALEA 475
                                               ****************************************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (479 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.64
//
[ok]

This GapMind analysis is from Apr 10 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