Alignments for a candidate for tyrB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for tyrB in Synechococcus elongatus PCC 7942

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Synpcc7942_1794 Synpcc7942_1794 succinyldiaminopimelate transaminase

Query= BRENDA::Q8YUK5
         (404 letters)



>FitnessBrowser__SynE:Synpcc7942_1794
          Length = 392

 Score =  521 bits (1341), Expect = e-152
 Identities = 259/403 (64%), Positives = 308/403 (76%), Gaps = 17/403 (4%)

Query: 2   QFSQRLHPLQSNVFADMDKAKSLALAAGKELIDLSLGSSDLPAEAHVIEAIAKSLYDPST 61
           + SQRL PLQ NVFADMD+AK++A+AAG+E+IDLSLGSSDLPA  HV+  IA SL DPST
Sbjct: 5   RLSQRLAPLQRNVFADMDRAKAVAIAAGREVIDLSLGSSDLPAPDHVVAVIAASLQDPST 64

Query: 62  HGYLLFNGTRDFRQAAANWYEQKFGVKVDPETEVLPLIGSQEGTAHLPLALLNPGDFALL 121
           HGYLL  GT  FRQ AA WYE+KFG+ VDPETEVL LIGSQEGTAHLPLA++ PG+ ALL
Sbjct: 65  HGYLLHQGTLPFRQVAAAWYERKFGLGVDPETEVLLLIGSQEGTAHLPLAVMEPGEIALL 124

Query: 122 LDPGYPSHAGGVYLASGQIYPMPLKAENDFLPVFADIPTDVLAQSRMMVLSYPHNPTAAI 181
            DPGYPSHAGGVYLA G+IY +P  A+  FLP F+ IPT++L++SR++VLSYPHNPT AI
Sbjct: 125 QDPGYPSHAGGVYLAGGEIYRLPTTADRGFLPDFSTIPTEILSRSRLLVLSYPHNPTTAI 184

Query: 182 APLSFFKEAVAFCQEHNIALVHDFPYVDMVFENAGNLNTNLPQSPIPNHQSLVPSILQAD 241
           APL+FF+EAVAFC+ H + L HDFPY D+ F+                    VPSI QAD
Sbjct: 185 APLAFFEEAVAFCRHHQLVLAHDFPYPDLGFDGVE-----------------VPSIFQAD 227

Query: 242 PDKSVSIEFFTLSKSYNMGGFRIGYAIGNAQMIQALRQIKAAVDFNQYRGILNGAIAALT 301
             K  +IEFF+LSKSYNMGGFR+G+AIGNA++I ALR++KA VDFNQY+GIL GAIAALT
Sbjct: 228 RQKQQAIEFFSLSKSYNMGGFRVGFAIGNAELIGALRRLKAVVDFNQYQGILAGAIAALT 287

Query: 302 GPQAGVEAAVSTFCQRRDAFINALHHIGWYVPTPKATMYIWAKLPSSWSQNSIEFCTQLV 361
           GPQA VEA    F  RRD FINAL   GW +P P +TMY+WA LP  W   S+EFC +LV
Sbjct: 288 GPQACVEATRQRFRDRRDIFINALAATGWTIPKPVSTMYLWAPLPEPWQTRSLEFCEKLV 347

Query: 362 RQTGVAASPGAGFGKSGEGYVRFALVHEPSILKIAVERMSNFL 404
            +TGVAASPG GFG  GEG+VRFALVH+   L+ A  R++ FL
Sbjct: 348 AETGVAASPGIGFGDCGEGFVRFALVHDRDRLEEAARRITQFL 390


Lambda     K      H
   0.320    0.135    0.405 

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: 546
Number of extensions: 25
Number of successful extensions: 2
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: 404
Length of database: 392
Length adjustment: 31
Effective length of query: 373
Effective length of database: 361
Effective search space:   134653
Effective search space used:   134653
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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