GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Pseudomonas fluorescens GW456-L13

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate PfGW456L13_3206 Aspartate aminotransferase (EC 2.6.1.1)

Query= CharProtDB::CH_088628
         (385 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3206
          Length = 396

 Score =  261 bits (667), Expect = 2e-74
 Identities = 152/369 (41%), Positives = 221/369 (59%), Gaps = 11/369 (2%)

Query: 19  VNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALA 78
           ++ +AL LR QG D++ L+ G+PDFDTP+ + + A  +L  G T YA   G   LREA+A
Sbjct: 20  IHYRALALREQGEDILLLSVGDPDFDTPQPIVQGAIDSLLNGNTHYAEVRGKRALREAIA 79

Query: 79  EKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGV 138
            + ++ +G SV+ ++  V  G + ALF++ Q +L+PGDEVIV  P +V+Y  +    G V
Sbjct: 80  RRHQQRSGQSVSADQVTVLAGAQCALFSVAQCVLNPGDEVIVAEPMYVTYEAVFGACGAV 139

Query: 139 VVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDF 198
           VV V    E GF   PE V   ITPRT+AL +NSP+NP+GA  P+    ALA L + HD 
Sbjct: 140 VVPVPVRSENGFRVLPEDVAARITPRTRALALNSPHNPSGASLPRSTWAALAELCIAHDL 199

Query: 199 YLVSDEIYEHLLYEGEHFSPGRV--APEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAM 256
           +L+SDE+Y  LL+EGEH SP  +    E T T+N  +K+ AMTGWR+G+   P  +   +
Sbjct: 200 WLISDEVYSELLFEGEHVSPASLPGMAERTATLNSLSKSHAMTGWRVGWVVAPPSLAAHL 259

Query: 257 ASVS-SQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLT-ALGLKA 314
            +++      SPD I Q A + AL   E++   +E  REAYR+RRDL+ + L    G++A
Sbjct: 260 ENLALCMLYGSPDFI-QDAAVVAL---ESNLPELEAMREAYRQRRDLVCDSLADCPGVRA 315

Query: 315 VRPSGAFYVLMDTSPIAPDEVRAAERLLEA-GVAVVPGTDF--AAFGHVRLSYATSEENL 371
           ++P G  +V++D           A+RLL+  GV+V+ G  F  +A GH+RL      E L
Sbjct: 316 LKPDGGMFVMLDIRQTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVVGAEPL 375

Query: 372 RKALERFAR 380
           R A +R AR
Sbjct: 376 RDACQRIAR 384


Lambda     K      H
   0.317    0.133    0.379 

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: 404
Number of extensions: 11
Number of successful extensions: 5
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: 385
Length of database: 396
Length adjustment: 31
Effective length of query: 354
Effective length of database: 365
Effective search space:   129210
Effective search space used:   129210
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