Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_012043944.1 BBTA_RS18110 aspartate--tRNA(Asp/Asn) ligase
Query= reanno::Phaeo:GFF2422 (592 letters) >NCBI__GCF_000015165.1:WP_012043944.1 Length = 590 Score = 837 bits (2161), Expect = 0.0 Identities = 391/587 (66%), Positives = 475/587 (80%), Gaps = 4/587 (0%) Query: 1 MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60 MH YR+HTC L SN+GETVRLSGW HR+RDHGG+LF+DLRDHYG+TQ + DPDS F Sbjct: 1 MHRYRTHTCGALRDSNIGETVRLSGWCHRIRDHGGVLFVDLRDHYGITQCVVDPDSKAFG 60 Query: 61 EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120 EK+RSEW +R++G V+ R E N ++PTG++E+++ DIEVLG + ELPL VFGEQEY Sbjct: 61 LAEKLRSEWVVRMEGKVRRRPEGTDNAELPTGQVELYVADIEVLGPAAELPLPVFGEQEY 120 Query: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180 PE+ RL+YR+LDLRREK+ +N++ R +I S+RRRM ++GF E+QTPI+TASSPEGARDF Sbjct: 121 PEDIRLKYRFLDLRREKLHQNIMTRGAIIDSMRRRMKEQGFFEFQTPILTASSPEGARDF 180 Query: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240 LVPSR+HPGKFYALPQAPQQ+KQL+M+SGFD+YFQIAPCFRDEDPRADR P +FYQLD+E Sbjct: 181 LVPSRIHPGKFYALPQAPQQYKQLLMMSGFDRYFQIAPCFRDEDPRADRLPGEFYQLDVE 240 Query: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQVSYKDAAKWYGTDKPDLRNPIKMQ 300 MSFV Q+DVF ++PV+ GVFE+F KG+ V WP++ + +A + YGTDKPDLRNPI+MQ Sbjct: 241 MSFVEQEDVFAAMEPVITGVFEDFAKGKPVTKGWPRIPFAEALRKYGTDKPDLRNPIEMQ 300 Query: 301 DCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFWR 360 D SEHFRGSGF +FA +LE+ ++ AIPAP GGSR FCDRMN +AQGEG PG+GYI WR Sbjct: 301 DVSEHFRGSGFKVFARMLEDTKNQVWAIPAPGGGSRAFCDRMNSWAQGEGQPGLGYIMWR 360 Query: 361 DQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARTVIGEE 420 + GEG AGPLA NIGPERT AIR QLG GDAAFF+ G P+ F AG ART +GEE Sbjct: 361 EGGEG---AGPLANNIGPERTAAIRTQLGTKEGDAAFFVAGDPEKFWKFAGLARTKVGEE 417 Query: 421 LGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDAL-LSDPLAVKGYQYD 479 L L DKDRFA WIVDFP+YE +E+ K+DF HNPFSMPQGG++AL DPL +K +QYD Sbjct: 418 LNLIDKDRFALAWIVDFPMYEYNEDDKKVDFSHNPFSMPQGGLEALQTKDPLTIKAFQYD 477 Query: 480 LACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCAAGI 539 +ACNGYE+ SG IRNHKPE M KAFEIAGYG++EV RFGGM AFQYGAPPHGG AAG+ Sbjct: 478 IACNGYEIASGGIRNHKPEAMVKAFEIAGYGEQEVVDRFGGMYRAFQYGAPPHGGMAAGV 537 Query: 540 DRMVMLLADEANIREVIMFPMNQRAEDLMMSAPSEPMSDQLMELGLR 586 DR+VMLL N+RE+ +FPMNQ+A DL+M APSE + QL EL +R Sbjct: 538 DRIVMLLCGTTNLREISLFPMNQQAMDLLMGAPSEATTKQLRELHIR 584 Lambda K H 0.320 0.139 0.423 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: 1164 Number of extensions: 43 Number of successful extensions: 4 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