Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_012115117.1 XAUT_RS15775 aspartate--tRNA(Asp/Asn) ligase
Query= uniprot:A0A2I7KAZ8 (592 letters) >NCBI__GCF_000017645.1:WP_012115117.1 Length = 623 Score = 812 bits (2097), Expect = 0.0 Identities = 394/621 (63%), Positives = 467/621 (75%), Gaps = 31/621 (4%) Query: 1 MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60 MH YRSHTC L+ + VGE VRLSGW HR+RDHGG+LFIDLRDHYG+TQV+ DPDS F Sbjct: 1 MHRYRSHTCGALSTAQVGEIVRLSGWCHRIRDHGGVLFIDLRDHYGLTQVVVDPDSAAFK 60 Query: 61 EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120 + EKVR+EW IRIDG V+ R E N + TG +EV+ ++EVLG S ELPL VFG+ EY Sbjct: 61 DAEKVRAEWVIRIDGKVRLRPEGTENPDLATGAVEVYATELEVLGPSAELPLPVFGDVEY 120 Query: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180 PEETRLRYR+LDLRREK+ +N++ R +I ++R RM +GF E+QTPI+TASSPEGARDF Sbjct: 121 PEETRLRYRFLDLRREKLHRNIMTRGAIIDAMRSRMKGQGFFEFQTPILTASSPEGARDF 180 Query: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240 LVPSRLHPGKFYALPQAPQQ+KQL+M+SGFD+YFQIAPCFRDEDPRADR P +FYQLDLE Sbjct: 181 LVPSRLHPGKFYALPQAPQQYKQLIMMSGFDRYFQIAPCFRDEDPRADRLPGEFYQLDLE 240 Query: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQISYKDAAKWYGTDKPDLRNPIKMQ 300 MSFV Q+D+F ++PV+ GVFE+F +G+ V +WP+I Y ++ + YGTDKPDLRNP+ MQ Sbjct: 241 MSFVEQEDIFAAVEPVITGVFEQFAEGKPVTQKWPRIPYAESLRKYGTDKPDLRNPLVMQ 300 Query: 301 DCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFWR 360 + SEHFRGSGF +FA +LE E E+ AIPAP GGSR FCDRMN +AQ EG PG+GYI WR Sbjct: 301 NVSEHFRGSGFKVFARMLEVEKNEVWAIPAPGGGSRAFCDRMNSWAQSEGQPGLGYIMWR 360 Query: 361 D------------------------QGE------GMEAAGPLAKNIGPERTEAIRQQLGL 390 D GE G+ AGPLA NIGPERTEAIR QL L Sbjct: 361 DLSADAAAGGEKAVKDALEKSRGPGAGEGHVVEPGVVGAGPLANNIGPERTEAIRAQLDL 420 Query: 391 GVGDAAFFLGGKPKTFESVAGRARIVIGEELGLTDKDRFAFCWIVDFPIYEKDEETGKID 450 GDAAFF+ G P F AG AR +GEEL L DKDRF WIVDFP YE EE K+D Sbjct: 421 KAGDAAFFVAGDPDKFVKFAGLARTRVGEELNLVDKDRFELAWIVDFPFYEYSEEEKKVD 480 Query: 451 FEHNPFSMPQGGMDAL-LSDPLAVKGYQYDLACNGYELVSGAIRNHKPEIMFKAFEIAGY 509 F HNPFSMPQGG+DAL DPL++K +QYD+ACNGYE+ SG IRNH+PE M KAFEIAGY Sbjct: 481 FSHNPFSMPQGGLDALNTQDPLSIKAFQYDIACNGYEIASGGIRNHRPEAMVKAFEIAGY 540 Query: 510 GKEEVEKRFGGMVNAFQYGAPPHGGCAAGIDRMVMLLADEANIREVIMFPMNQRAEDLMM 569 + VE+RFGGM AFQYGAPPHGG AAG+DR+VMLL N+RE+ +FPMNQ+A DL+M Sbjct: 541 DAQTVEERFGGMYRAFQYGAPPHGGMAAGVDRIVMLLCGVTNLREISLFPMNQQALDLLM 600 Query: 570 AAPSEPMSDQLMELGLRVIPQ 590 AP+E QL EL +R PQ Sbjct: 601 GAPAEAAPKQLRELHIRPAPQ 621 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: 1215 Number of extensions: 53 Number of successful extensions: 3 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: 623 Length adjustment: 37 Effective length of query: 555 Effective length of database: 586 Effective search space: 325230 Effective search space used: 325230 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