GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8500245
          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:

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