Alignments for a candidate for PPYAT in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for PPYAT in Crocosphaera subtropica ATCC 51142

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_009547075.1 CCE_RS04895 LL-diaminopimelate aminotransferase

Query= BRENDA::Q8YUK5
         (404 letters)



>NCBI__GCF_000017845.1:WP_009547075.1
          Length = 395

 Score =  578 bits (1491), Expect = e-170
 Identities = 284/404 (70%), Positives = 326/404 (80%), Gaps = 16/404 (3%)

Query: 1   MQFSQRLHPLQSNVFADMDKAKSLALAAGKELIDLSLGSSDLPAEAHVIEAIAKSLYDPS 60
           M F+ RL  L+ NVFADMD+AKS A++ GK +IDLSLGSSDLPA+   I+AIA SL DPS
Sbjct: 1   MHFANRLQALEKNVFADMDRAKSQAISNGKTIIDLSLGSSDLPADQEAIKAIASSLEDPS 60

Query: 61  THGYLLFNGTRDFRQAAANWYEQKFGVKVDPETEVLPLIGSQEGTAHLPLALLNPGDFAL 120
           THGYLL +GT  FR+  A WY+++FGV+VDP TEVL LIGSQEGTAHLPLALL+PGDFAL
Sbjct: 61  THGYLLHHGTLKFRETVAQWYDKRFGVEVDPHTEVLTLIGSQEGTAHLPLALLDPGDFAL 120

Query: 121 LLDPGYPSHAGGVYLASGQIYPMPLKAENDFLPVFADIPTDVLAQSRMMVLSYPHNPTAA 180
           LLDPGYPSHAGGVYLA GQIYPMPL AENDFLPVFAD+P+ VL Q++MMVLSYPHNPT A
Sbjct: 121 LLDPGYPSHAGGVYLAGGQIYPMPLLAENDFLPVFADVPSQVLEQAKMMVLSYPHNPTTA 180

Query: 181 IAPLSFFKEAVAFCQEHNIALVHDFPYVDMVFENAGNLNTNLPQSPIPNHQSLVPSILQA 240
            A L FF++AVAFCQEH + LVHDFPYVD+VFE                     PSILQA
Sbjct: 181 TASLGFFEQAVAFCQEHGLVLVHDFPYVDIVFEG----------------MVQPPSILQA 224

Query: 241 DPDKSVSIEFFTLSKSYNMGGFRIGYAIGNAQMIQALRQIKAAVDFNQYRGILNGAIAAL 300
           DP KS+SIEFFTLSKSYNMGGFRIGYAIGN ++IQALR++KA VDFNQYRGILNGAIAAL
Sbjct: 225 DPTKSLSIEFFTLSKSYNMGGFRIGYAIGNLEIIQALRRVKAVVDFNQYRGILNGAIAAL 284

Query: 301 TGPQAGVEAAVSTFCQRRDAFINALHHIGWYVPTPKATMYIWAKLPSSWSQNSIEFCTQL 360
            G Q  VE  V+ F  RRDAFI ALH+IGW+V  P+ATMY+WAKLP +W   S+EFCT+L
Sbjct: 285 NGDQTTVERTVTRFQTRRDAFIKALHNIGWHVTPPQATMYVWAKLPQAWENKSVEFCTEL 344

Query: 361 VRQTGVAASPGAGFGKSGEGYVRFALVHEPSILKIAVERMSNFL 404
           V  TGVA SPGAGFGK GEGYVRFALVH+P IL++AV+++  FL
Sbjct: 345 VAATGVAVSPGAGFGKQGEGYVRFALVHDPDILELAVQKIDQFL 388


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: 584
Number of extensions: 32
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: 395
Length adjustment: 31
Effective length of query: 373
Effective length of database: 364
Effective search space:   135772
Effective search space used:   135772
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 Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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