GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Desulfovibrio vulgaris Miyazaki F

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>lcl|FitnessBrowser__Miya:8500245 DvMF_1002
           adenosylmethionine-8-amino-7-oxononanoate
           aminotransferase (RefSeq)
          Length = 491

 Score =  164 bits (416), Expect = 4e-45
 Identities = 130/404 (32%), Positives = 198/404 (49%), Gaps = 48/404 (11%)

Query: 33  GSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNV-FTNEPALRLAH 91
           G+R+ D  G   +D    +  NV GH HP L AA+  Q +K+ H + +   +EP++ LA 
Sbjct: 58  GNRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGSEPSIELAA 117

Query: 92  KL--VDATFAERVFFCNSGAEANEAAFKLA-----RRVAHDRFGTEKYEIVAALNSFHGR 144
           +L  +      RVF+ +SG+ + E A K+A     +  AH      +   ++  N++HG 
Sbjct: 118 RLAAIAPQGLTRVFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFLSLRNAYHGD 177

Query: 145 TLFTVNVGGQSKYSDGFGPKI--TGITHVPY------------------NDLAALKAAVS 184
           T+  V +GG + +   + P +  T     PY                    +  L A   
Sbjct: 178 TVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSCERECITHMETLFARHG 237

Query: 185 DKTCAVVLEP-IQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQH 243
            + CA V+EP +QG  G+L     +L+  RELCD H   LV DEV  G G++G LFA + 
Sbjct: 238 HELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVAVGFGKTGTLFACEQ 297

Query: 244 YGVTPDILTSAKSLGGGF-PIAAMLTTED-----LAKHLVVGT--HGTTYGGNPLACAVA 295
            GVTPD L  AK + GG+ P+AA LTTE      LA+H  + T  HG TY GNPLACA A
Sbjct: 298 EGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTFFHGHTYTGNPLACAAA 357

Query: 296 EAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGC-VLSDAWKGKA 354
            A +DV     V+  +  K  +   RL+ + +   +  ++R  G++ G  ++ +    +A
Sbjct: 358 IASLDVFEEERVMERLQPKIARLAARLDTLRDLPHV-GDIRQRGVMTGIEMVRNRATKEA 416

Query: 355 KD--------IFNAAEREGLMILQAGPDVIRFAPSLVVEDADID 390
            D        +   A R G++I   G DV+   P L + D +ID
Sbjct: 417 YDLALRVGHRVTLEARRRGVIIRPLG-DVMVLMPPLSITDDEID 459


Lambda     K      H
   0.320    0.136    0.400 

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: 459
Number of extensions: 27
Number of successful extensions: 6
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: 406
Length of database: 491
Length adjustment: 33
Effective length of query: 373
Effective length of database: 458
Effective search space:   170834
Effective search space used:   170834
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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