Alignments for a candidate for aspS2 in Roseburia faecis M72

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Roseburia faecis M72

Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_022047122.1 M72_RS06730 aspartate--tRNA ligase

Query= reanno::Phaeo:GFF2422
         (592 letters)



>NCBI__GCF_001406815.1:WP_022047122.1
          Length = 582

 Score =  563 bits (1452), Expect = e-165
 Identities = 294/589 (49%), Positives = 392/589 (66%), Gaps = 18/589 (3%)

Query: 4   YRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFAEIE 63
           YR  T  ++++ ++G+T+R++GWV  +RDHGG+ FIDLRD Y V Q++          +E
Sbjct: 5   YRDVTLNQVSEQDIGKTIRVAGWVENIRDHGGVSFIDLRDMYAVMQIVIRDGKL----LE 60

Query: 64  KVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKS-EELPLMVFGEQEYP- 121
            +R E  I ++G ++ RDE   N KIPTG IE+  +++ VLG+   +LP  V   +    
Sbjct: 61  GIRKEQAITVEGLIEKRDEETYNPKIPTGTIELDAKEVTVLGEVYSQLPFEVMTSKSVVH 120

Query: 122 EETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDFL 181
           E+ RL+YRYLDLR +K++ N++ RS +I  +R +M   GF E QTPI+ ASSPEGARD++
Sbjct: 121 EDVRLKYRYLDLRNQKVKDNIIFRSKVISYLREKMTSMGFLELQTPILCASSPEGARDYI 180

Query: 182 VPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLEM 241
           VPSR   GKFYALPQAPQQ+KQL+MVSGFDKYFQIAPCFRDED RADRSP +FYQLD EM
Sbjct: 181 VPSRKFKGKFYALPQAPQQYKQLLMVSGFDKYFQIAPCFRDEDARADRSPGEFYQLDFEM 240

Query: 242 SFVTQQDVFDTIQPVMQGVFEEFGKGRKV--DSEWPQVSYKDAAKWYGTDKPDLRNPIKM 299
           SF TQ+DVF   + V+  VFE+F     V   + +P +SYK A   +G+DKPDLRNP+++
Sbjct: 241 SFATQEDVFAVGEEVLSSVFEKFAPEGSVVTKAPYPIISYKQAMLEFGSDKPDLRNPLRI 300

Query: 300 QDCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFW 359
            D ++ F+   F  F       G  +RAI      S+ F +++ KFA G G+ G+GY+  
Sbjct: 301 IDVTDFFQKCTFKPFI------GKTVRAIRVHADMSKGFHEKLLKFATGLGMGGLGYLEV 354

Query: 360 RDQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARTVIGE 419
            + G      GP+ K I  +  E  R   GL VGD  FF+  K +     AG  R  +GE
Sbjct: 355 LEDG---SYKGPIDKFIPDDCKEEFRTLAGLEVGDTIFFMADKEERAAYYAGMIRNELGE 411

Query: 420 ELGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDAL-LSDPLAVKGYQY 478
           +L L +K+ + FC++ DFP++EKD ET KI F HNPFSMPQGG++AL   DPL +  YQY
Sbjct: 412 KLDLIEKNAYRFCYVNDFPMFEKDPETKKIGFTHNPFSMPQGGLEALNTMDPLDILAYQY 471

Query: 479 DLACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCAAG 538
           D+ CNG EL SGA+RNH  +IM KAFEIAGY KE ++ +FG +  AFQYGAPPH G A G
Sbjct: 472 DIVCNGVELSSGAVRNHDMQIMEKAFEIAGYDKEVLKNKFGALYTAFQYGAPPHAGMAPG 531

Query: 539 IDRMVMLLADEANIREVIMFPMNQRAEDLMMSAPSEPMSDQLMELGLRV 587
           +DRM+MLL +E NIREVI FPMN  A+DLM  AP+E    QL E+ ++V
Sbjct: 532 VDRMIMLLRNEENIREVIAFPMNGNAQDLMCGAPNEVTEQQLREVHIKV 580


Lambda     K      H
   0.320    0.139    0.423 

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: 1023
Number of extensions: 49
Number of successful extensions: 7
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: 592
Length of database: 582
Length adjustment: 37
Effective length of query: 555
Effective length of database: 545
Effective search space:   302475
Effective search space used:   302475
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 Jul 25 2024. The underlying query database was built on Jul 25 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