Alignments for a candidate for lysN in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for lysN in Pseudomonas fluorescens FW300-N2C3

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate AO356_25355 AO356_25355 aspartate aminotransferase

Query= SwissProt::P58350
         (410 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25355
          Length = 404

 Score =  422 bits (1084), Expect = e-122
 Identities = 205/393 (52%), Positives = 280/393 (71%)

Query: 17  RISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTA 76
           R++    S   +I  R A  + +G  +I L AGEPDFDTP+H+++AA +AI +G T+YT 
Sbjct: 11  RLARAQSSATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHIREAAIEAIGQGHTRYTQ 70

Query: 77  LDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWT 136
           + G   L++A+  KF++ENGL     +  V  G KQ+++NA+ A+LD GD+VI+P PYW 
Sbjct: 71  VAGVRSLREAVAAKFRQENGLDVTWQDTLVCNGGKQVIYNALAATLDEGDQVIVPAPYWV 130

Query: 137 SYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADY 196
           SY ++V +C G+  ++ CDA SGF+LT   L+AAITP+TRW++LNSPSNP+GA YS  + 
Sbjct: 131 SYPEMVQLCGGESRIVTCDADSGFKLTPAALDAAITPQTRWLILNSPSNPTGAVYSREEL 190

Query: 197 RPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGW 256
           + L +VLL HPHV +L DD+YEH+++D   F T AQ+EP L +RTLT+NGVSKAYAMTGW
Sbjct: 191 QALADVLLAHPHVLILADDIYEHLIFDDQVFYTLAQVEPRLASRTLTMNGVSKAYAMTGW 250

Query: 257 RIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVV 316
           RIG+A GPR L++AM  +Q Q TS  SSISQ A++AAL+GP+DF++E    FQRRRDL+V
Sbjct: 251 RIGFATGPRWLLEAMEKLQGQQTSGASSISQQAALAALDGPKDFIRESRAVFQRRRDLMV 310

Query: 317 NGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGS 376
             LNA  GL C  P GAFY F+ CAG++G+ +  G+ + TD D    LL++A VAVV GS
Sbjct: 311 ALLNATPGLACASPGGAFYAFASCAGLIGRTSSGGRVLHTDEDVAHALLDEADVAVVHGS 370

Query: 377 AFGLSPFFRISYATSEAELKEALERIAAACDRL 409
           AFGL P+ RI+YA  +A L++A E I   CD L
Sbjct: 371 AFGLGPYIRIAYALDDASLRQACEAIRGFCDAL 403


Lambda     K      H
   0.318    0.134    0.393 

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: 485
Number of extensions: 18
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: 410
Length of database: 404
Length adjustment: 31
Effective length of query: 379
Effective length of database: 373
Effective search space:   141367
Effective search space used:   141367
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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, or view the source code.

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 catabolism of small carbon sources