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:

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:

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:

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:

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