Alignments for a candidate for aspS2 in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Methylovulum miyakonense HT12

Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_019865998.1 METMI_RS0109240 aspartate--tRNA ligase

Query= SwissProt::Q51422
         (591 letters)



>NCBI__GCF_000384075.1:WP_019865998.1
          Length = 595

 Score =  781 bits (2016), Expect = 0.0
 Identities = 384/586 (65%), Positives = 467/586 (79%), Gaps = 3/586 (0%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MR+H CG+L+    G+ VT+CGWVHRRRDHGGVIF+D+RDR GL QVV DPD    FA A
Sbjct: 1   MRTHKCGELDTQQLGETVTICGWVHRRRDHGGVIFIDLRDRAGLVQVVIDPDTEAAFAAA 60

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
           + VRSE+V+KI+G VR RP G  N NM SG+IE+L  E+EVLN++ETPPFP++   +V E
Sbjct: 61  EHVRSEYVLKISGIVRHRPGGTVNANMRSGAIEILAKEIEVLNESETPPFPIESEIEVNE 120

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
           E RLRYR+IDLRR  M  K+K+R  +T  +R +LDDN F ++ETP L + TPEGARDY+V
Sbjct: 121 ELRLRYRYIDLRRVAMQEKMKVRRDVTRVLRNFLDDNEFFEIETPYLTKATPEGARDYIV 180

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSRT+   FFALPQSPQL+KQ+LMVAG DRYYQ+ +CFRDEDLRADRQPEFTQ+DIETSF
Sbjct: 181 PSRTHVNSFFALPQSPQLYKQILMVAGMDRYYQVVRCFRDEDLRADRQPEFTQLDIETSF 240

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300
           + E  I+ I E+M+RQLF +V++V    EFP M ++EAM R+G D+PDLRIPLELVDVA+
Sbjct: 241 MTEDQIMAIMEEMIRQLFAKVINVALPAEFPRMTYQEAMSRFGIDRPDLRIPLELVDVAE 300

Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAA-SMPRSQIDDYTKFVGIYGAKGLAYIKVNE 359
            LK+VEFKVFSGPANDPKGRV A+RVPGA   + R  ID+ TK+VGIYGAKGLAYIKVN+
Sbjct: 301 DLKDVEFKVFSGPANDPKGRVVAMRVPGAGEKLSRKDIDELTKYVGIYGAKGLAYIKVND 360

Query: 360 RAKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD 419
            A G+EGLQSPIVKF P      I+ + GA +GD++FFGADK  IV +A+GALR+K+GHD
Sbjct: 361 LAAGLEGLQSPIVKFAPAEAWASIMAKTGAQNGDLLFFGADKTSIVNEAMGALRVKLGHD 420

Query: 420 LKLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMV 478
           L L+  EW P+WVVDFPMF+ +   G  +A+HHPFT+P C+  +L ANPGAALSRAYD+V
Sbjct: 421 LNLIEGEWQPVWVVDFPMFDWDEKSGRYNAIHHPFTAPSCSVEDLVANPGAALSRAYDLV 480

Query: 479 LNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDR 538
           LNGTE+GGGSIRI+  +MQQ VF +LGI E E +EKFGFLLDALKYGAPPHGGLAFGLDR
Sbjct: 481 LNGTEVGGGSIRINRPAMQQTVFGILGIGEEEAQEKFGFLLDALKYGAPPHGGLAFGLDR 540

Query: 539 LVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRL 584
           LVMLMTG+ SIR+VIAFPKTQSA   +  AP  V  + L+EL IRL
Sbjct: 541 LVMLMTGSHSIRDVIAFPKTQSAACPLVSAPAVVSDEQLKELGIRL 586


Lambda     K      H
   0.321    0.140    0.411 

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: 1081
Number of extensions: 37
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: 591
Length of database: 595
Length adjustment: 37
Effective length of query: 554
Effective length of database: 558
Effective search space:   309132
Effective search space used:   309132
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: 53 (25.0 bits)

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