Alignments for a candidate for aspS2 in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Herbaspirillum seropedicae SmR1

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 HSERO_RS00990 HSERO_RS00990 aspartyl-tRNA synthetase

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__HerbieS:HSERO_RS00990
          Length = 601

 Score =  759 bits (1961), Expect = 0.0
 Identities = 385/597 (64%), Positives = 459/597 (76%), Gaps = 9/597 (1%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MR+ YCG   E+L GQ V+LCGWVHRRRDHGGVIF+D+RDREGL QVV DPDRA+ F  A
Sbjct: 3   MRTQYCGLTTEALLGQTVSLCGWVHRRRDHGGVIFIDLRDREGLVQVVCDPDRADVFKNA 62

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
           + VR+EF ++ITG VR RPEG  N N+ SG IEVL +ELEVLN + TPPF LD+ S + E
Sbjct: 63  ESVRNEFCLRITGLVRNRPEGTTNANLKSGKIEVLCHELEVLNPSVTPPFQLDDDS-LSE 121

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
            TRL +R +DLRRP+M   L+LR ++   +R++LD  GF+D+ETP+L + TPEGARDYLV
Sbjct: 122 TTRLTHRVLDLRRPQMQNNLRLRYKVAMEVRKFLDAQGFIDIETPMLTKSTPEGARDYLV 181

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSR   G FFALPQSPQLFKQLLMVA FDRYYQI KCFRDEDLRADRQPEFTQID ETSF
Sbjct: 182 PSRVNAGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRADRQPEFTQIDCETSF 241

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300
           L+E +I  + E M+R +FK  LD++  + FP M F  AM +YGSDKPD+R+ LE  ++ D
Sbjct: 242 LNEQEIRDLFEGMIRLVFKNALDIDLPNPFPVMDFATAMGKYGSDKPDMRVKLEFTELTD 301

Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360
            +K+VEFKVFSG AN   GRV  LRVPG A MPRS+ID YT+FV IYGAKGLAYIKVNE+
Sbjct: 302 VMKDVEFKVFSGAANSEGGRVVGLRVPGGAEMPRSEIDAYTQFVAIYGAKGLAYIKVNEK 361

Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD- 419
           AKG +GLQSPIVK I +A LN IL++ GA DGD++FFGADKAK+V DA+GALR+K+GH  
Sbjct: 362 AKGRDGLQSPIVKNIHDAALNAILEKTGAQDGDLIFFGADKAKVVNDAIGALRVKIGHSE 421

Query: 420 ----LKLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAE-LEANPGAALSR 473
                 L    W P+WVVDFPMFE ++DG    ALHHPFTSPK    + +  NPGAA+++
Sbjct: 422 FGKKNGLFDDAWRPLWVVDFPMFEYDEDGQRWVALHHPFTSPKDGHEDFISTNPGAAIAK 481

Query: 474 AYDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLA 533
           AYDMVLNG ELGGGS+RIH   +Q  VFR L ID+ E + KFGFLLDAL+YGAPPHGG+A
Sbjct: 482 AYDMVLNGWELGGGSVRIHRADVQSKVFRALKIDDEEAKLKFGFLLDALQYGAPPHGGIA 541

Query: 534 FGLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKA 590
           FGLDRLV +M GA SIR+VIAFPKTQ A  ++T AP  VD K LRELHIRLR    A
Sbjct: 542 FGLDRLVTMMAGAESIRDVIAFPKTQRAQCLLTHAPSEVDEKQLRELHIRLRNTEPA 598


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: 1108
Number of extensions: 48
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: 591
Length of database: 601
Length adjustment: 37
Effective length of query: 554
Effective length of database: 564
Effective search space:   312456
Effective search space used:   312456
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