Alignments for a candidate for serA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Dyella japonica UNC79MFTsu3.2

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::Q9I6H5
         (409 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3581
          Length = 410

 Score =  522 bits (1344), Expect = e-153
 Identities = 259/409 (63%), Positives = 325/409 (79%), Gaps = 2/409 (0%)

Query: 3   KTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEYLKTALSGDELKERIADAHFIGIRSR 62
           KTS  K+ IK LLLEGV Q+AV+  + AGY+ IE+ + +L   ELK RIA+AH +GIRSR
Sbjct: 2   KTSYPKADIKVLLLEGVSQSAVEVFRRAGYSQIEFHEKSLPEAELKARIAEAHIVGIRSR 61

Query: 63  TQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAIL 122
           + LT +V + A++LIAVGCFCIGTNQVDL  AR++G+ VFNAPYSNTRSVAELV+AEAI+
Sbjct: 62  SHLTADVLEQARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAELVIAEAIM 121

Query: 123 LLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEALGMQVFFYDT 182
           LLRGIP+KNA CHRGGW KSAA SFE+R K LGIVGYG IGTQ+ VLAE+LGM+V F+D 
Sbjct: 122 LLRGIPQKNALCHRGGWTKSAAGSFEVRDKVLGIVGYGHIGTQVGVLAESLGMRVIFHDI 181

Query: 183 VTKLPLGNAVQIGSLHELLGMSDIVSLHVPELPSTQWMIGEKEIRAMKKGGILINAARGT 242
            TKL LGNA   GSL +LL  +D+V+LHVPE P+T+ MIG  E+  M+KG  LINA+RGT
Sbjct: 182 ETKLSLGNARAAGSLDDLLERADVVTLHVPETPATKLMIGATELAKMRKGAALINASRGT 241

Query: 243 VVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFASPLRGLDRVILTPHIGGSTAEAQA 302
           VV++D LAAA++  H+ GAA+DVFP+EPK ND+ F SPL G+D VILTPHIGGST EAQ 
Sbjct: 242 VVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVGMDNVILTPHIGGSTLEAQD 301

Query: 303 NIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHANIPGVMSEINKVFADN 362
           NIG+EVA KLV+YSDNG+++S+VNFPEV LP HP   RLLHIH N+PGV+S IN++F+  
Sbjct: 302 NIGIEVASKLVRYSDNGSTLSAVNFPEVTLPEHPNSRRLLHIHRNVPGVLSRINELFSAG 361

Query: 363 GINVSGQYLQTNEKVGYVVIDVDAEYSDLAL--EKLQQVNGTIRSRVLF 409
            IN+  Q+LQT+ +VGYVVIDV A+ +      ++L  + GT+RSRVL+
Sbjct: 362 NINIDAQFLQTDSQVGYVVIDVSADEAQAGALKDRLAAIPGTLRSRVLY 410


Lambda     K      H
   0.317    0.135    0.381 

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: 477
Number of extensions: 11
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: 409
Length of database: 410
Length adjustment: 31
Effective length of query: 378
Effective length of database: 379
Effective search space:   143262
Effective search space used:   143262
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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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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