Alignments for a candidate for aspS2 in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Thermomonospora curvata DSM 43183

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_012852474.1 TCUR_RS10510 aspartate--tRNA(Asn) ligase

Query= curated2:Q9Y9U7
         (442 letters)



>NCBI__GCF_000024385.1:WP_012852474.1
          Length = 436

 Score =  349 bits (896), Expect = e-101
 Identities = 185/425 (43%), Positives = 265/425 (62%), Gaps = 9/425 (2%)

Query: 22  VRVCGWAYRIRDLGRLKFILVRDRSGVIQATVKRGESPEDALRAAEDLKLESVVCVEGEL 81
           V VCGW   +R   +++F+++RD +G++Q T KRG   ++  +A E L  ES V + G +
Sbjct: 17  VTVCGWVNALRLQRKMQFVILRDPTGMVQITHKRGGEGDELEQAIEALTTESAVVITGRV 76

Query: 82  RQAPTRE--GVEVKVERLEVLSTPVEPLPLEVEGSEKASLPTRLKYRWLDIR-NPMVSAI 138
              P  +  G+E+  ER+EV+      LP++    EK+ +  RL +R+LDIR  P    +
Sbjct: 77  VDNPIVKLGGLEIVPERVEVVGKAEASLPID----EKSGMEHRLDWRFLDIRLRPSSRLL 132

Query: 139 FELEAMVAKVFRDYYWSQGFVEIFTPKIVAAGTESGAEVFPVVYFDKTAFLAQSPQFYKQ 198
           F+++       R+Y +++GF E+ TPK++   +ESGAEVF + YF   A+LAQSPQFYKQ
Sbjct: 133 FDVQTTFEAGLREYAYAEGFTEMHTPKLMGTASESGAEVFKLGYFGGDAYLAQSPQFYKQ 192

Query: 199 FAVIAGLERVFEIGPVFRAEPHHTSRHLNEYHSLDIEVGFIESYNDVMNYVEGFM-RAIV 257
            AV AG+ERVFEIGPVFRAEP  TSRH  E+  +D+E+ +I+   DVM + E  +  AI 
Sbjct: 193 MAVAAGIERVFEIGPVFRAEPSFTSRHATEFTGVDVEMAWIDDVEDVMAFEERMLAHAIA 252

Query: 258 RMLEEDGRRVLELYGVELPRIPASGIPKIPLRKAYEILEEKYGKKVEYGEDLDSEGERLM 317
           ++ +  G  + E YGV+L ++P    P++ + +A EIL  +        EDLD EGER +
Sbjct: 253 KVADVHGEAIREHYGVDL-KVPTVPFPRLTMAEAQEILRARGWDPAGEKEDLDPEGERAI 311

Query: 318 GAYAGEELDSDFVFIVEYPWKVRPFYTMRKDDEPSWTYSFDLLYRGLEIVTGGQREHRYH 377
            A+  E+   +FVFI  YP  +RPFY MR  D P  T SFDLL++GLE+ TG QREHRY 
Sbjct: 312 SAHIAEQTGHEFVFITHYPASIRPFYHMRPKDRPDLTLSFDLLWKGLEVTTGAQREHRYD 371

Query: 378 RLLENLRDKGLDAESFQFYLDFFKHGAPPHGGAGMGLERIVMQTLKLENIREARMLPRDT 437
            L +   +KGLD    Q Y++ F+ G PPHGG GMGL R+++  L L++IREA  L R  
Sbjct: 372 VLCKQAAEKGLDTAPMQDYMNIFRFGTPPHGGLGMGLGRLLVAMLNLDSIREATFLFRGP 431

Query: 438 ERITP 442
            R+TP
Sbjct: 432 NRLTP 436


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: 508
Number of extensions: 16
Number of successful extensions: 5
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: 436
Length adjustment: 32
Effective length of query: 410
Effective length of database: 404
Effective search space:   165640
Effective search space used:   165640
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_012852474.1 TCUR_RS10510 (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.22873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-120  389.3   0.0   1.5e-120  389.0   0.0    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012852474.1  TCUR_RS10510 aspartate--tRNA(Asn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012852474.1  TCUR_RS10510 aspartate--tRNA(Asn) ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.0   0.0  1.5e-120  1.5e-120       7     428 .]      10     436 .]       5     436 .] 0.94

  Alignments for each domain:
  == domain 1  score: 389.0 bits;  conditional E-value: 1.5e-120
                                 TIGR00458   7 keekdgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvavkGkvk 75 
                                                ++ d + v++ gwv  +r + ++ fv+lrd  g++qi+ k+   ++el + i+ l +es v+++G+v 
  lcl|NCBI__GCF_000024385.1:WP_012852474.1  10 RDHLD-QTVTVCGWVNALRLQRKMQFVILRDPTGMVQITHKRGGEGDELEQAIEALTTESAVVITGRVV 77 
                                               44444.78***********************************************************99 PP

                                 TIGR00458  76 eke.kapqgleiipeklevlneakeplPldleekveaeldtrldarfldlr.rpkvqaifkirsevles 142
                                                +     +glei+pe++ev+ +a+++lP+d   k  + ++ rld rfld+r rp+ + +f +++     
  lcl|NCBI__GCF_000024385.1:WP_012852474.1  78 DNPiVKLGGLEIVPERVEVVGKAEASLPIDE--K--SGMEHRLDWRFLDIRlRPSSRLLFDVQTTFEAG 142
                                               77615689*********************85..4..46789**********8899************** PP

                                 TIGR00458 143 vreflaeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPifra 211
                                               +re+ + egf+e++tPkl+++a+e G+e+f++ yf ++a+laqsPq+ykq+ +aag+erv+ei+P+fra
  lcl|NCBI__GCF_000024385.1:WP_012852474.1 143 LREYAYAEGFTEMHTPKLMGTASESGAEVFKLGYFGGDAYLAQSPQFYKQMAVAAGIERVFEIGPVFRA 211
                                               ********************************************************************* PP

                                 TIGR00458 212 eehntkrhlnevisidiemafedh.kdvldileelvvrvfedvaeklkkel.evlevklevpeeklerl 278
                                               e + t rh +e++++d+ema+ d+ +dv+   e+++ +++ +va+   +++ e  +v+l+vp  +++rl
  lcl|NCBI__GCF_000024385.1:WP_012852474.1 212 EPSFTSRHATEFTGVDVEMAWIDDvEDVMAFEERMLAHAIAKVADVHGEAIrEHYGVDLKVPTVPFPRL 280
                                               ************************9******************998777653789************** PP

                                 TIGR00458 279 tydeaieilrakG.keikdgedlsteaekllG....ekmdgly.fitdfPteikPfytmPdednPeisk 341
                                               t  ea eilra+G  + ++ edl  e e+++     e+ + ++ fit +P+ i+Pfy m ++d+P+ + 
  lcl|NCBI__GCF_000024385.1:WP_012852474.1 281 TMAEAQEILRARGwDPAGEKEDLDPEGERAISahiaEQTGHEFvFITHYPASIRPFYHMRPKDRPDLTL 349
                                               *************446899***********998887666665559************************ PP

                                 TIGR00458 342 sfdllyrdleissGaqrihdydllvekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmvlldl 410
                                               sfdll+++le+++Gaqr h yd+l  +  +kGl+   +++y++ f++G PPh G G+G+ rl +++l+l
  lcl|NCBI__GCF_000024385.1:WP_012852474.1 350 SFDLLWKGLEVTTGAQREHRYDVLCKQAAEKGLDTAPMQDYMNIFRFGTPPHGGLGMGLGRLLVAMLNL 418
                                               ********************************************************************* PP

                                 TIGR00458 411 knireavlfPrdrkrltP 428
                                               + irea+++ r ++rltP
  lcl|NCBI__GCF_000024385.1:WP_012852474.1 419 DSIREATFLFRGPNRLTP 436
                                               ****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (436 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: 11.90
//
[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