GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:208056
          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 (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