Alignments for a candidate for aspS2 in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Pyrolobus fumarii 1A

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate WP_014026192.1 PYRFU_RS03160 aspartate--tRNA(Asn) ligase

Query= curated2:Q9Y9U7
         (442 letters)



>NCBI__GCF_000223395.1:WP_014026192.1
          Length = 476

 Score =  408 bits (1049), Expect = e-118
 Identities = 220/455 (48%), Positives = 297/455 (65%), Gaps = 24/455 (5%)

Query: 5   RFIADIIASKESLVGGRVRVCGWAYRIRDLGRLKFILVRDRSGVIQATVKRGESPEDALR 64
           R+IAD++  +E  VG +  + GW   +R  G + F++VRDRSG +Q   K+  + E A  
Sbjct: 29  RYIADVL--REGRVGEKYVIAGWVEAVRRHGGVVFVVVRDRSGRMQVVAKKNVARE-AWE 85

Query: 65  AAEDLKLESVVCVEGELRQAPTR-EGVEVKVERLEVLSTPVEPLPLEVEGSEKASLPTRL 123
            A +L  ESV+ V+G L ++     G E++ E + VL+   EPLP+E  G + ASL  RL
Sbjct: 86  TARELSRESVIAVKGVLVESKAALGGKELQAEEILVLNE-AEPLPIE-PGGKTASLAIRL 143

Query: 124 KYRWLDIRNPMVSAIFELEAMVAKVFRDYYWSQGFVEIFTPKIVAAGTESGAEVFPVVYF 183
           +YRW+D+R P  +      A+ A+    ++  QGF+EIFTPKIVA+ TE GAEVFP++YF
Sbjct: 144 RYRWIDLREPRHATPIIAAAVAAEAASKFFAEQGFIEIFTPKIVASATEGGAEVFPIIYF 203

Query: 184 DKTAFLAQSPQFYKQFAVIAGLERVFEIGPVFRAEPHHTSRHLNEYHSLDIEVGFIESYN 243
           +K AFLAQSPQ YKQ  VI+GLERV+EIGP FRAE HHT RHL E+ S+D E+GFI+SY 
Sbjct: 204 EKEAFLAQSPQLYKQMGVISGLERVYEIGPAFRAEKHHTVRHLTEFTSVDFEMGFIKSYE 263

Query: 244 DVMNYVEGFMRAIVRMLEEDGRR---VLELYGVELPRIPASGIPKIPLRKAYEILEEKYG 300
           DVM  VEG + A++  ++ D R    + E Y   L   P    P++P+ +AY +L E  G
Sbjct: 264 DVMKVVEGAVTAMIEAIQSDPRTKPLLEEYYPQALELKPPREYPRVPIDEAYRLLREA-G 322

Query: 301 KKVEYGEDLDSEGERLMGAYAGEELDSDFVFIVEYPWKVRPFYTMRKDDEPSW------- 353
            ++E  EDL +EGE+ +G    +E  +  VF+  YPW VRPFYTM+  +EP W       
Sbjct: 323 LEIEEDEDLGTEGEKKLGEIYEKEYGAPLVFVTMYPWSVRPFYTMKAREEP-WSCPEEPR 381

Query: 354 ------TYSFDLLYRGLEIVTGGQREHRYHRLLENLRDKGLDAESFQFYLDFFKHGAPPH 407
                 TYSFDLL++GLE+ TGGQREH    L E LR+KGL+  +F +YL+ F+HGAPPH
Sbjct: 382 FTNPKRTYSFDLLFKGLEVATGGQREHCPRILEEQLREKGLNPAAFDWYLEMFRHGAPPH 441

Query: 408 GGAGMGLERIVMQTLKLENIREARMLPRDTERITP 442
           GGAG+GLER+VMQ L L NIREAR +PRD E + P
Sbjct: 442 GGAGIGLERVVMQLLGLGNIREARFVPRDPEHLKP 476


Lambda     K      H
   0.321    0.140    0.414 

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: 635
Number of extensions: 34
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: 442
Length of database: 476
Length adjustment: 33
Effective length of query: 409
Effective length of database: 443
Effective search space:   181187
Effective search space used:   181187
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_014026192.1 PYRFU_RS03160 (aspartate--tRNA(Asn) ligase)
to HMM TIGR00458 (aspS: aspartate--tRNA(Asn) ligase (EC 6.1.1.23))

# 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/TIGR00458.hmm
# target sequence database:        /tmp/gapView.23655.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00458  [M=428]
Accession:   TIGR00458
Description: aspS_nondisc: aspartate--tRNA(Asn) ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-128  414.7   0.0   3.5e-128  414.1   0.0    1.2  1  lcl|NCBI__GCF_000223395.1:WP_014026192.1  PYRFU_RS03160 aspartate--tRNA(As


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014026192.1  PYRFU_RS03160 aspartate--tRNA(Asn) ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.1   0.0  3.5e-128  3.5e-128       3     428 .]      31     476 .]      29     476 .] 0.91

  Alignments for each domain:
  == domain 1  score: 414.1 bits;  conditional E-value: 3.5e-128
                                 TIGR00458   3 sadi.keekdgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvav 70 
                                                ad+  e + g++ ++ gwv  +r  G+++fv++rdr g +q+++kk  v +e  +++++l +esv+av
  lcl|NCBI__GCF_000223395.1:WP_014026192.1  31 IADVlREGRVGEKYVIAGWVEAVRRHGGVVFVVVRDRSGRMQVVAKK-NVAREAWETARELSRESVIAV 98 
                                               56651445667999****************************98876.588999*************** PP

                                 TIGR00458  71 kGkvkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkirsev 139
                                               kG + e+++a +g e+  e++ vlnea eplP+++  k+ a l  rl +r +dlr+p+  +     +  
  lcl|NCBI__GCF_000223395.1:WP_014026192.1  99 KGVLVESKAALGGKELQAEEILVLNEA-EPLPIEPGGKT-ASLAIRLRYRWIDLREPRHATPIIAAAVA 165
                                               *************************98.6******9995.899**************987776666677 PP

                                 TIGR00458 140 lesvreflaeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPi 208
                                                e+  +f+ae+gfie+ tPk+vasateGG+e+f+i yfe+eaflaqsPqlykq+ + +glervyei+P 
  lcl|NCBI__GCF_000223395.1:WP_014026192.1 166 AEAASKFFAEQGFIEIFTPKIVASATEGGAEVFPIIYFEKEAFLAQSPQLYKQMGVISGLERVYEIGPA 234
                                               89999**************************************************************** PP

                                 TIGR00458 209 fraeehntkrhlnevisidiemafedh.kdvldileelvvrvfedvaeklkk.....elevlevklevp 271
                                               frae+h+t rhl+e++s+d em f +  +dv++++e  v+ ++e ++   ++     e+  + ++l +p
  lcl|NCBI__GCF_000223395.1:WP_014026192.1 235 FRAEKHHTVRHLTEFTSVDFEMGFIKSyEDVMKVVEGAVTAMIEAIQSDPRTkplleEYYPQALEL-KP 302
                                               ************************9998*****************998765535544344444444.47 PP

                                 TIGR00458 272 eeklerltydeaieilrakGkeikdgedlsteaekllGekmdgly.....fitdfPteikPfytm.... 331
                                               + +++r+  dea  +lr +G ei++ edl te ek lGe+++ +y     f+t +P  ++Pfytm    
  lcl|NCBI__GCF_000223395.1:WP_014026192.1 303 PREYPRVPIDEAYRLLREAGLEIEEDEDLGTEGEKKLGEIYEKEYgaplvFVTMYPWSVRPFYTMkare 371
                                               899***********************************9999988777779**************5555 PP

                                 TIGR00458 332 .....Pde...dnPeisksfdllyrdleissGaqrihdydllvekikakGlePeslksyleafkyGmPP 392
                                                    P+e    nP+++ sfdll+++le+++G qr h   +l e++++kGl+P +++ yle f++G PP
  lcl|NCBI__GCF_000223395.1:WP_014026192.1 372 epwscPEEprfTNPKRTYSFDLLFKGLEVATGGQREHCPRILEEQLREKGLNPAAFDWYLEMFRHGAPP 440
                                               544442223336899****************************************************** PP

                                 TIGR00458 393 haGwGlGaerlvmvlldlknireavlfPrdrkrltP 428
                                               h G G+G+er+vm ll+l nirea + Prd++ l+P
  lcl|NCBI__GCF_000223395.1:WP_014026192.1 441 HGGAGIGLERVVMQLLGLGNIREARFVPRDPEHLKP 476
                                               *********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (476 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.58
//
[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