Alignments for a candidate for gatB in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Leptospirillum ferrooxidans C2-3

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_014450044.1 LFE_RS09705 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000284315.1:WP_014450044.1
          Length = 505

 Score =  402 bits (1033), Expect = e-116
 Identities = 213/490 (43%), Positives = 304/490 (62%), Gaps = 19/490 (3%)

Query: 70  YEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVRL 129
           YE V+G+E H QL T TK FC C N +G+ PNT  CPVC+G PG LPV+N + +  G+RL
Sbjct: 17  YEMVVGLEVHSQLLTKTKMFCRCENRFGAEPNTLTCPVCLGYPGVLPVMNERALRLGIRL 76

Query: 130 GLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGHRRFGI 189
           GLAL C +  KS FDRK YFYPDLPKGYQISQFD P+ +GG + +  P       +   I
Sbjct: 77  GLALGCSIHRKSFFDRKHYFYPDLPKGYQISQFDHPLLTGGSISLLGP----DAGKTIRI 132

Query: 190 TRVHMEEDAGKLLHSDTGDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACEMQRIARY 249
            R+HMEEDAGK LH+   D S VDLNRAGVPLLEIVSEPD+RS  EA  Y  ++++I R 
Sbjct: 133 HRIHMEEDAGKNLHAGLADSSHVDLNRAGVPLLEIVSEPDIRSPSEAVSYLKQLRQILRA 192

Query: 250 LGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEISRQALLYN 309
            GVS+GNM+EGS RCD N+S+R  G++ FG KVE+KN+N+F  + +A+ +E SRQ+ L +
Sbjct: 193 SGVSDGNMEEGSFRCDANVSLRLRGESRFGVKVEVKNMNSFRFVQKALVYEFSRQSELLD 252

Query: 310 QGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDSIRASLPE 369
           +G  ++I +ETRL++ G  +T+ MR KE   DYR+FPEPD+P V   +E++D  R +LPE
Sbjct: 253 RG--ERIRSETRLFDTGNGRTLPMRSKEEALDYRFFPEPDIPMVFFPEEWIDEERKNLPE 310

Query: 370 LPEAKR-RRYEAMGLGMQDVLFLANDVSVAEYFDAVIG--------KGAEVKLAANWIMS 420
           LPE K  R    +G+   D   L  +  +  +F+  +         +G E+    + ++ 
Sbjct: 311 LPEEKAIRLARELGIDPSDARTLVFEEELVVFFEEALSHFEPMSKVRGFELSKGRSRLLH 370

Query: 421 DIAAYLKNEKLSINDIKLT----PQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKG 476
            + + +  E     D  L+     Q LA ++A + D ++S    KE+    L        
Sbjct: 371 FVLSEVLREWNRRGDAALSSGGAAQGLAHILAGVMDESLSLNQAKEVYLLSLDLEQHPSE 430

Query: 477 MIKAKDLVQITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPG 536
           +IK K   Q++    +   + +++SENPK++  + SGK +L G+  GQVMK S GKANP 
Sbjct: 431 VIKEKGFAQVSGEGALSAWIDEMISENPKEVSDFCSGKDRLLGFLVGQVMKKSAGKANPQ 490

Query: 537 LLNKILLEKL 546
            +N+++ +KL
Sbjct: 491 KVNELIRQKL 500


Lambda     K      H
   0.317    0.134    0.379 

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: 682
Number of extensions: 40
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: 550
Length of database: 505
Length adjustment: 35
Effective length of query: 515
Effective length of database: 470
Effective search space:   242050
Effective search space used:   242050
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_014450044.1 LFE_RS09705 (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.29462.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-165  535.6   0.0   5.5e-165  535.4   0.0    1.0  1  lcl|NCBI__GCF_000284315.1:WP_014450044.1  LFE_RS09705 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000284315.1:WP_014450044.1  LFE_RS09705 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.4   0.0  5.5e-165  5.5e-165       3     480 ..      16     500 ..      14     501 .. 0.97

  Alignments for each domain:
  == domain 1  score: 535.4 bits;  conditional E-value: 5.5e-165
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               +ye+v+GlEvH ql tk+K+Fc+c+n++   +pNt +cpvclg+PG+lPv+N++a++  + l+lal++ 
  lcl|NCBI__GCF_000284315.1:WP_014450044.1  16 KYEMVVGLEVHSQLLTKTKMFCRCENRFGA-EPNTLTCPVCLGYPGVLPVMNERALRLGIRLGLALGCS 83 
                                               89**************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                               i   +s FdRKhYfYpDlPkgyqi+q+d P+ ++G++++   +  k+i+i+r+h+EeD+gk+ +++   
  lcl|NCBI__GCF_000284315.1:WP_014450044.1  84 IH-RKSFFDRKHYFYPDLPKGYQISQFDHPLLTGGSISLLGPDAGKTIRIHRIHMEEDAGKNLHAGL-- 149
                                               65.69************************************************************77.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               ++ s vD+NR+gvPLlEiV++Pd++s+ ea+ +lk+lrqilr +++sdg++eeGs+R+D+Nvs+rl+G+
  lcl|NCBI__GCF_000284315.1:WP_014450044.1 150 ADSSHVDLNRAGVPLLEIVSEPDIRSPSEAVSYLKQLRQILRASGVSDGNMEEGSFRCDANVSLRLRGE 218
                                               579****************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               +++g +vE+KN+ns++ ++ka+ yE  Rq++ll +ge +  etr fd+ + +t+ +R+Kee+ DYR+fp
  lcl|NCBI__GCF_000284315.1:WP_014450044.1 219 SRFGVKVEVKNMNSFRFVQKALVYEFSRQSELLDRGERIRSETRLFDTGNGRTLPMRSKEEALDYRFFP 287
                                               ********************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep.. 345
                                               ePd+p++ + ee+++e  +++lpelPe+k irl +e+g++ +da++lv ++el+  fee+ +  ++   
  lcl|NCBI__GCF_000284315.1:WP_014450044.1 288 EPDIPMVFFPEEWIDE-ERKNLPELPEEKAIRLARELGIDPSDARTLVFEEELVVFFEEALSHFEPMsk 355
                                               ****************.9**********************************99999999988877677 PP

                                 TIGR00133 346 ..........klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen 404
                                                             +++l+e+l+e n++      +  +++ la++++ + ++ +s  +ake+    l+ 
  lcl|NCBI__GCF_000284315.1:WP_014450044.1 356 vrgfelskgrSRLLHFVLSEVLREWNRRGDAALSSGGAAQGLAHILAGVMDESLSLNQAKEVYLLSLDL 424
                                               788888887778899*************99999999999****************************** PP

                                 TIGR00133 405 kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkeve 473
                                               +++p+++i+++g  q+s e +l + ++e+i+enpkev ++ sgk+++l+flvGqvmkk+ g+a+p++v+
  lcl|NCBI__GCF_000284315.1:WP_014450044.1 425 EQHPSEVIKEKGFAQVSGEGALSAWIDEMISENPKEVSDFCSGKDRLLGFLVGQVMKKSAGKANPQKVN 493
                                               ********************************************************************* PP

                                 TIGR00133 474 kllkell 480
                                               +l++++l
  lcl|NCBI__GCF_000284315.1:WP_014450044.1 494 ELIRQKL 500
                                               ***9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (505 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: 7.44
//
[ok]

This GapMind analysis is from Apr 10 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