Alignments for a candidate for aspS2 in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Phaeobacter inhibens BS107

Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate GFF2422 PGA1_c24530 aspartyl-tRNA synthetase AspS

Query= reanno::Phaeo:GFF2422
         (592 letters)



>FitnessBrowser__Phaeo:GFF2422
          Length = 592

 Score = 1216 bits (3146), Expect = 0.0
 Identities = 592/592 (100%), Positives = 592/592 (100%)

Query: 1   MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60
           MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA
Sbjct: 1   MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60

Query: 61  EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120
           EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY
Sbjct: 61  EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120

Query: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180
           PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF
Sbjct: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180

Query: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240
           LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE
Sbjct: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240

Query: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQVSYKDAAKWYGTDKPDLRNPIKMQ 300
           MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQVSYKDAAKWYGTDKPDLRNPIKMQ
Sbjct: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQVSYKDAAKWYGTDKPDLRNPIKMQ 300

Query: 301 DCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFWR 360
           DCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFWR
Sbjct: 301 DCSEHFRGSGFAIFANLLENEGTEIRAIPAPKGGSRKFCDRMNKFAQGEGLPGMGYIFWR 360

Query: 361 DQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARTVIGEE 420
           DQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARTVIGEE
Sbjct: 361 DQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARTVIGEE 420

Query: 421 LGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDALLSDPLAVKGYQYDL 480
           LGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDALLSDPLAVKGYQYDL
Sbjct: 421 LGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDALLSDPLAVKGYQYDL 480

Query: 481 ACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCAAGID 540
           ACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCAAGID
Sbjct: 481 ACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGAPPHGGCAAGID 540

Query: 541 RMVMLLADEANIREVIMFPMNQRAEDLMMSAPSEPMSDQLMELGLRVIPQDQ 592
           RMVMLLADEANIREVIMFPMNQRAEDLMMSAPSEPMSDQLMELGLRVIPQDQ
Sbjct: 541 RMVMLLADEANIREVIMFPMNQRAEDLMMSAPSEPMSDQLMELGLRVIPQDQ 592


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: 1415
Number of extensions: 47
Number of successful extensions: 1
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: 592
Length adjustment: 37
Effective length of query: 555
Effective length of database: 555
Effective search space:   308025
Effective search space used:   308025
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 09 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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