Alignments for a candidate for aspS2 in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Shewanella loihica PV-4

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 5209622 Shew_2079 aspartyl-tRNA synthetase (RefSeq)

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__PV4:5209622
          Length = 592

 Score =  775 bits (2000), Expect = 0.0
 Identities = 381/591 (64%), Positives = 464/591 (78%), Gaps = 1/591 (0%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MRSHYCG +N S  G+EVTL GWV+R RD GGV+FLD+RDREG+ QVV+DPD  E F  A
Sbjct: 1   MRSHYCGDVNRSHVGEEVTLVGWVNRSRDLGGVVFLDLRDREGVIQVVYDPDLPEVFDVA 60

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
             +RSEF V++ G VR RP+   N  M +G IEVLG  L +LN A   P  +D+     E
Sbjct: 61  STLRSEFCVQVKGLVRARPDSQINDQMRTGEIEVLGKALTILNSAPALPINMDKNQHNTE 120

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
           E RL+YR++DLRRPEMA ++  R+++TS++RR+LD NGFLD+ETPIL + TPEGARDYLV
Sbjct: 121 EQRLKYRYLDLRRPEMAERIIFRSKVTSAVRRFLDGNGFLDIETPILTKATPEGARDYLV 180

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSRTY G FFALPQSPQLFKQLLM++GFDRYYQI KCFRDEDLRADRQPEFTQIDIETSF
Sbjct: 181 PSRTYKGQFFALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDIETSF 240

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301
           +  + ++  TE+MVR LFKE+L+V+  EFP M F EAMRRYGSDKPDLR PLELVDVAD 
Sbjct: 241 MTSAQVMDKTEEMVRGLFKELLNVDLGEFPKMTFAEAMRRYGSDKPDLRNPLELVDVADL 300

Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361
           +K+V+FKVF  PAND +GRVA L VPG AS+ R Q+D+Y K+V IYGAKGLA++KVNE  
Sbjct: 301 VKDVDFKVFQEPANDSEGRVAVLCVPGGASLSRKQLDEYGKYVNIYGAKGLAWMKVNELE 360

Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421
            G+EG+QSP++KF+ E  +  IL+R GA +GD++ FGADKA IV +A+GALR+KVG D  
Sbjct: 361 NGLEGIQSPVLKFLSEEVVKGILERTGAANGDLILFGADKANIVAEAMGALRLKVGEDFD 420

Query: 422 LLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPK-CTPAELEANPGAALSRAYDMVLN 480
           LL  +W P+WVVDFPMFE   DG L A+HHPFT+P   TPAELEA+P AA+S AYDMVLN
Sbjct: 421 LLQGDWKPLWVVDFPMFERTSDGGLHAMHHPFTAPSGITPAELEADPTAAISDAYDMVLN 480

Query: 481 GTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540
           G ELGGGS+RI+D  MQ AVFR+LGI++ E +EKFGFLL+ALKYG PPH GLAFGLDR+V
Sbjct: 481 GCELGGGSVRIYDAEMQSAVFRILGINDEEAQEKFGFLLEALKYGTPPHAGLAFGLDRMV 540

Query: 541 MLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591
           MLMTGASSIR+V+AFPKT +A   +T APG  +   L EL + + E  K +
Sbjct: 541 MLMTGASSIRDVMAFPKTTTAACPLTNAPGFANPVQLEELGVSVVEAKKEQ 591


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: 1083
Number of extensions: 40
Number of successful extensions: 2
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: 592
Length adjustment: 37
Effective length of query: 554
Effective length of database: 555
Effective search space:   307470
Effective search space used:   307470
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