GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Desulfovibrio vulgaris Hildenborough

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase

Query= SwissProt::Q8ZPV2
         (408 letters)



>lcl|MicrobesOnline__882:208056 DVU2559
           adenosylmethionine--8-amino-7-oxononanoate
           aminotransferase
          Length = 542

 Score =  172 bits (437), Expect = 2e-47
 Identities = 137/416 (32%), Positives = 202/416 (48%), Gaps = 57/416 (13%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH---IGNGY 78
           P I    +G+ L D  G  Y+D    +  N  GH HP + EA+  Q +R  H   +G G 
Sbjct: 84  PCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAHSTLLGLGG 143

Query: 79  TNEPALRLAKKL--IDATFAERVFFCNSGAEANEAALKLARKYAHDRVGN--HKSGIVAF 134
           T  P++ LA +L  I      RVF+ +SG+ A EAALK+A +Y          ++ ++AF
Sbjct: 144 T--PSIELAARLTAIAPAGLTRVFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAF 201

Query: 135 KNAFHGRTLFTVSAGGQPTYSQDFAPL---------------PPDIRH-----AAYNDLN 174
            NA+HG T+ +VS GG   +   + PL               P D+R      A   ++ 
Sbjct: 202 SNAYHGDTIGSVSLGGMSLFHGIYGPLLFDPVRAPAPHCYRCPADLRPETCGMACLGEVE 261

Query: 175 SASALIDDNTCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTG 233
                     CAV+VEP VQG  G++   + +L+GLR+LCDRH   ++ DEV  G G+TG
Sbjct: 262 RLMRHHGHELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGKTG 321

Query: 234 ELYAYMHYGVTPDILTTAKALGGGF-PIGAMLTTQ--------DYASVMTPGTHGTTYGG 284
            ++A    GV PD+L  AK + GG+ P+ A L T+         YA   T   HG TY G
Sbjct: 322 TMFACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRT-FFHGHTYTG 380

Query: 285 NPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFG---MFSEIRGLGLLLGC 341
           N LA A A   LD+         +R R    IERL TL           +IR +G++ G 
Sbjct: 381 NALACAAALASLDVFEEERTLETLRPR----IERLATLLAPLNDLPHVGDIRRVGVMTGI 436

Query: 342 VL------QTEFAGKAKL---IAQEAAKAGVMVLIAGGDVVRFAPALNVSDEEIAT 388
            L      +T +  + ++   +  EA + GV+V    GDV+   P L++++ E+ T
Sbjct: 437 ELVADRETRTPYRPEERIGHRVTLEARRRGVIVRPL-GDVMVLMPPLSITETELET 491


Lambda     K      H
   0.320    0.137    0.413 

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: 636
Number of extensions: 37
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: 408
Length of database: 542
Length adjustment: 33
Effective length of query: 375
Effective length of database: 509
Effective search space:   190875
Effective search space used:   190875
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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