Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_083924252.1 D471_RS0118415 aspartate--tRNA ligase
Query= uniprot:A0A2I7KAZ8 (592 letters) >NCBI__GCF_000341125.1:WP_083924252.1 Length = 590 Score = 664 bits (1712), Expect = 0.0 Identities = 331/592 (55%), Positives = 425/592 (71%), Gaps = 15/592 (2%) Query: 1 MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60 MH YR+H+C +L K +VG+ VRLSGWVH RD GGLLF+DLRDHYGVTQ+MA P+SPVF Sbjct: 1 MHRYRTHSCGQLRKEHVGQQVRLSGWVHNRRDLGGLLFVDLRDHYGVTQLMARPESPVFE 60 Query: 61 EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120 ++ ++ E IR+ G V AR + VN +PTGEIE+ ++EVLG +EELPL VF E Sbjct: 61 QLSRISKESVIRVTGQVAARSDENVNPGLPTGEIEIEATEMEVLGTTEELPLTVFPEDNT 120 Query: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180 EE RL YR+LDLRRE+M +N++LRS ++ SIR++M D GFNE+QTPI+T+SSPEGARDF Sbjct: 121 SEERRLGYRFLDLRRERMHRNIMLRSQVVASIRQKMTDLGFNEFQTPILTSSSPEGARDF 180 Query: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240 LVPSRLHPG+F+ALPQAPQQFKQL+MV+GFD+YFQIAPCFRDED RADRSP +FYQLD+E Sbjct: 181 LVPSRLHPGRFFALPQAPQQFKQLLMVAGFDRYFQIAPCFRDEDSRADRSPGEFYQLDVE 240 Query: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQISYKDAAKWYGTDKPDLRNPIKMQ 300 MSFV Q+DVF+ I+ VM VF EF G ++ S +P+I+Y+DA +WYGTDKPDLR P++M Sbjct: 241 MSFVEQEDVFEVIEKVMTDVFREFSDGWEITSPYPRIAYRDALEWYGTDKPDLRVPMRML 300 Query: 301 DCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGS--RKFCDRMNKFAQGEGLPGMGYIF 358 D + F + F F EG ++RA+ P+ G RKF D + FA +G G+ Sbjct: 301 DVTALFDKTDFRAF------EGKKVRALAVPRVGDKPRKFFDGIGDFAVEQGAKGLA--- 351 Query: 359 WRDQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKT-FESVAGRARIVI 417 W GE E GP+AK + E ++ + LG G G FF + + + R+ Sbjct: 352 WLKVGENGELTGPIAKFV-TEISDELLSTLGAGPGYGLFFCASEDEAEINRIMAPVRVEA 410 Query: 418 GEELGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDAL-LSDPLAVKGY 476 G+ L ++ + FCWIVDFP++E +E+ G + F HNPFSMPQGGM+AL DPL + + Sbjct: 411 GKRADLFEEKVYRFCWIVDFPMFEINEQ-GDVAFSHNPFSMPQGGMEALNTQDPLDILAW 469 Query: 477 QYDLACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCA 536 QYD+ CNG EL SGAIRNH PEIM+KAF+IAGY KE VE FGGM+ A ++GAPPHGG A Sbjct: 470 QYDIVCNGVELSSGAIRNHSPEIMYKAFDIAGYDKEAVEAEFGGMLRALKFGAPPHGGIA 529 Query: 537 AGIDRMVMLLADEANIREVIMFPMNQRAEDLMMAAPSEPMSDQLMELGLRVI 588 G+DR+VMLLADE NIRE I FP+NQ A+DLMM APS QL ++ +R + Sbjct: 530 PGVDRIVMLLADEPNIRETIAFPLNQNAQDLMMGAPSAVSDQQLHDVHIRTV 581 Lambda K H 0.321 0.139 0.424 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: 1072 Number of extensions: 46 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: 592 Length of database: 590 Length adjustment: 37 Effective length of query: 555 Effective length of database: 553 Effective search space: 306915 Effective search space used: 306915 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.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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