Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_020920939.1 RHE_RS07635 aspartate--tRNA ligase
Query= reanno::Phaeo:GFF2422 (592 letters) >NCBI__GCF_000092045.1:WP_020920939.1 Length = 596 Score = 803 bits (2074), Expect = 0.0 Identities = 379/591 (64%), Positives = 464/591 (78%), Gaps = 2/591 (0%) Query: 1 MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60 MH YRSHTCA L K++VG TVR++GWVHRVRDHGG+LFIDLRDHYG+TQV+ADPDSP F Sbjct: 1 MHRYRSHTCAALRKTDVGSTVRIAGWVHRVRDHGGVLFIDLRDHYGITQVVADPDSPAFK 60 Query: 61 EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120 E VR EW IRIDG VKAR E VN + TGEIE++ ++IEVL ++ELPL VFGE EY Sbjct: 61 MAETVRGEWVIRIDGLVKARTEDTVNKTMATGEIELYAQEIEVLSAAKELPLPVFGEPEY 120 Query: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180 PE+ RL+YR+LDLRRE + KN++ R+ +I ++RR M GF EY TPI+TASSPEGARDF Sbjct: 121 PEDVRLKYRFLDLRRETLHKNIVKRTQVISAMRREMGSAGFTEYTTPILTASSPEGARDF 180 Query: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240 LVPSR+HPG FYALPQAPQQ+KQL+MV+GFD+YFQIAPCFRDEDPRADR P +FYQLDLE Sbjct: 181 LVPSRIHPGTFYALPQAPQQYKQLLMVAGFDRYFQIAPCFRDEDPRADRLPGEFYQLDLE 240 Query: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQVSYKDAAKWYGTDKPDLRNPIKMQ 300 MSFVTQ+DV++T+ P+M VFEEF +G+ V EWP++ Y +A + YG+DKPDLRNPI M+ Sbjct: 241 MSFVTQEDVWNTMGPLMTKVFEEFAEGKPVTKEWPRIPYDEAIRKYGSDKPDLRNPIVME 300 Query: 301 DCSEHFRGSGFAIFANLL-ENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFW 359 +EHF GSGF +FA ++ N ++ AIPA GGSR FCDRMN +AQ +G PG+GYIFW Sbjct: 301 AVTEHFAGSGFKVFAGMIASNPKVQVWAIPAKTGGSRAFCDRMNAWAQSQGQPGLGYIFW 360 Query: 360 RDQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARTVIGE 419 R +G+ +E AGPLAKNIG ERT+AIR QLGL GDA FF+ G+P+ F AG ART GE Sbjct: 361 RKEGDKLEGAGPLAKNIGEERTDAIRTQLGLDDGDACFFVAGEPEKFYKFAGEARTKAGE 420 Query: 420 ELGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDALLS-DPLAVKGYQY 478 EL L D+DRF CWIVDFP +E ++E K+DF HNPFSMPQGG+DAL + DPL +K +QY Sbjct: 421 ELNLVDRDRFELCWIVDFPFFEWNDEEKKVDFAHNPFSMPQGGLDALQNQDPLTIKAFQY 480 Query: 479 DLACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCAAG 538 D CNG+E+ SG+IRN PE M AFE G +++VE RFGG+ AFQYGAPPHGG A G Sbjct: 481 DAVCNGFEIASGSIRNQSPETMVAAFEKVGLSQQDVEDRFGGLYRAFQYGAPPHGGAAFG 540 Query: 539 IDRMVMLLADEANIREVIMFPMNQRAEDLMMSAPSEPMSDQLMELGLRVIP 589 IDR++MLL N+RE+ +FPMNQ+A+DL+M APS QL EL +R IP Sbjct: 541 IDRIIMLLVGAKNLREISLFPMNQQAQDLLMGAPSPATLTQLRELAIRPIP 591 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: 1149 Number of extensions: 48 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: 596 Length adjustment: 37 Effective length of query: 555 Effective length of database: 559 Effective search space: 310245 Effective search space used: 310245 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