Alignments for a candidate for aspS2 in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Acidimicrobium ferrooxidans DSM 10331

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_015797990.1 AFER_RS02725 aspartate--tRNA ligase

Query= curated2:A4X5Y3
         (607 letters)



>NCBI__GCF_000023265.1:WP_015797990.1
          Length = 588

 Score =  504 bits (1299), Expect = e-147
 Identities = 279/586 (47%), Positives = 371/586 (63%), Gaps = 20/586 (3%)

Query: 2   IRTHDAGSLRATDAGSTVTLAGWVARRRDHGG-VIFVDLRDGSGVAQVVLREEDAHVLRN 60
           +RTH  G+L  +     V++ GWVAR R+HG  ++FVD+RD +G  Q V+    +  L  
Sbjct: 12  LRTHYIGALDESLLDRDVSVCGWVARIREHGEHLVFVDVRDHTGTVQCVMDGRGS--LHT 69

Query: 61  EYCVRVTGEVTRRPEGNENPELATGEVEVTAEELEVLSEAAPLPLPVDDQIEAGDDVRLR 120
           E  VR+ G+V RRPEG EN +LATG +E+  +  EVL +A PLPLP+D+  E  +  RLR
Sbjct: 70  EAAVRIEGQVARRPEGTENTDLATGAIELRVQHAEVLGDADPLPLPLDEHAEVEETTRLR 129

Query: 121 YRYLDLRRSGPASALRLRSAANQIARTVLHERDFLEIETPTLTRSTPEGARDFLVPVRLQ 180
           +RYLDLRR+     LR R+A N   R  +  + F+E+ETP L   TPEGAR+FLVP R Q
Sbjct: 130 WRYLDLRRARMQRNLRARAATNAAIRRAMEAQGFVEVETPLLWTPTPEGAREFLVPSRTQ 189

Query: 181 PGTWYALPQSPQLFKQLLMVGGMERYYQIARCYRDEDFRADRQPEFTQLDIEMSFVTEDD 240
           PG+ Y+LPQSPQ+ KQLLM+GG++RYYQIARC RDED RADRQ EFTQLD+E SFVT++D
Sbjct: 190 PGSVYSLPQSPQIAKQLLMIGGVDRYYQIARCLRDEDLRADRQFEFTQLDLEASFVTQED 249

Query: 241 VIDLGEAIVSRLWRELAGHQITRPIPRITWHEAMARYGSDKPDLRYGVELTELTDYLRGT 300
           V     A +  + R + G     PI  ITWHEAM R+GSDKPD R+G+EL ++T+ +R +
Sbjct: 250 VRSFVSAAIREVIRSVRGVDDV-PIGTITWHEAMTRWGSDKPDRRFGMELVDVTEAVRDS 308

Query: 301 RFRVFAGAIEAGGYVGAVVMPGGAAQSRKELDGWQDWAKARGAKGLAYVVLDAETG-EAR 359
             R       A  YV A+V+      SR  LD     A++ GAKGLA+  +++ T  E  
Sbjct: 309 GARAL-----AADYVTALVV--AEPLSRSRLDELTQRARSAGAKGLAWFRVESRTPLEIA 361

Query: 360 GPVAKNLSTEHLAGLADVVGAKPGDAIFFAAGAESRAAQELLGAARVEIARRANLVDESA 419
            P+AK ++   L  L +  GA+ GD I   A      A   LG  R+ + R  +L D  A
Sbjct: 362 SPLAKAMTPAALEALVERTGAEVGDTILVVAD-RFEVACTALGTIRLALGR--HLADPDA 418

Query: 420 WAFCWVVDAPMFERVTDREEAGAGGWTAVHHPFTAPNAEWMDRFEEAPDRALAYAYDIVC 479
               WV+D P+FE V D      G   + HHPFT P+A+ MD  E  P R  + +YD+V 
Sbjct: 419 LDVFWVIDFPLFEGVDDE-----GHLVSAHHPFTMPHADDMDLLEREPLRVRSQSYDLVM 473

Query: 480 NGNEIGGGSIRIHRGDVQQRVFDLLGITPEQARDKFGFLLEAFKYGPPPHGGIAFGWDRV 539
           NG E+G GSIRIHR D+Q ++F LLG+  + A D+FGFLL+AF++GPPPHGG AFG DR+
Sbjct: 474 NGWELGSGSIRIHRPDLQAQIFGLLGLDEQAAADRFGFLLDAFRFGPPPHGGFAFGIDRL 533

Query: 540 CMLLAGADSIREVIAFPKTRGGFDPLTAAPTPITAAQRLEAGVDAR 585
             LL G ++IREVIAFPKT+ G DP+T AP P+        G++AR
Sbjct: 534 VALLLGEETIREVIAFPKTQSGQDPMTGAPKPVDDGVLAALGLEAR 579


Lambda     K      H
   0.319    0.137    0.415 

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: 886
Number of extensions: 44
Number of successful extensions: 8
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: 607
Length of database: 588
Length adjustment: 37
Effective length of query: 570
Effective length of database: 551
Effective search space:   314070
Effective search space used:   314070
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 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