GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Pseudomonas fluorescens FW300-N1B4

Align Aspartate/prephenate aminotransferase; AspAT / PAT; Transaminase A; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate Pf1N1B4_5070 Aspartate aminotransferase (EC 2.6.1.1)

Query= SwissProt::Q02635
         (400 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5070
          Length = 404

 Score =  461 bits (1185), Expect = e-134
 Identities = 222/397 (55%), Positives = 286/397 (72%)

Query: 4   LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63
           L   L+  +PSAT  +  +  E +A+G  +I L AGEPDFDTP ++++AAI AI+ G T+
Sbjct: 8   LNQRLASAQPSATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHVREAAIHAIEHGHTR 67

Query: 64  YTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAP 123
           YT V+G+  LREA+A KF+REN LD +   T+V  GGKQ+++NA  ATLN GD+V++PAP
Sbjct: 68  YTQVAGVRSLREAVAAKFRRENGLDVSWQDTLVCNGGKQVIYNALAATLNEGDQVIVPAP 127

Query: 124 YWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSH 183
           YWVSYPEMV LCGG    V    +  FKL    L  AITP+T+W + NSPSNP+GA YS 
Sbjct: 128 YWVSYPEMVQLCGGEARIVTCDADTGFKLTPAALAAAITPQTRWLILNSPSNPTGAVYSE 187

Query: 184 EELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAM 243
            EL+AL  VL+ HPHV +L DD+YEHL + D  F T  +VEP L  RTLTMNGVSKAYAM
Sbjct: 188 TELRALAAVLLDHPHVLILADDIYEHLIFDDQAFYTLAQVEPRLAPRTLTMNGVSKAYAM 247

Query: 244 TGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRD 303
           TGWRIG+A GP  L++AM+ +QGQQTSGA+S++Q AA+ AL GP+DFI  ++  FQ RRD
Sbjct: 248 TGWRIGFATGPRWLLEAMEKLQGQQTSGASSVSQQAALAALEGPKDFIRESRAAFQARRD 307

Query: 304 LVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVV 363
           L+V++LN   G+ C +P GAFY + SCA LIG+T+P+G+V+ TDED    LL+   VAVV
Sbjct: 308 LMVTLLNDTPGLECVSPAGAFYAFASCARLIGRTSPAGRVLHTDEDVAHALLDEADVAVV 367

Query: 364 HGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
           HGSAFGLGP  RI+YA  +A L +AC  I+ FC A R
Sbjct: 368 HGSAFGLGPYIRIAYALDDASLRQACEAIRAFCTALR 404


Lambda     K      H
   0.318    0.134    0.402 

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: 473
Number of extensions: 19
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: 400
Length of database: 404
Length adjustment: 31
Effective length of query: 369
Effective length of database: 373
Effective search space:   137637
Effective search space used:   137637
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