GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Sphingobium czechense LL01

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_066608605.1 V473_RS18720 diaminobutyrate--2-oxoglutarate transaminase

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



>NCBI__GCF_001046645.1:WP_066608605.1
          Length = 436

 Score =  140 bits (352), Expect = 9e-38
 Identities = 119/393 (30%), Positives = 189/393 (48%), Gaps = 42/393 (10%)

Query: 36  VW--DQSGRELIDFAGGIAVNVLGHAHPALVAALTEQA--NKLWHVSNVFTNEPALRLAH 91
           VW  D  G   +DF  G +    GH HP L  AL +    + + H  ++ T+  A  LA 
Sbjct: 43  VWMHDNQGGRYLDFLSGCSTLNYGHNHPVLKNALVDYIVNDGITHGLDLHTDAKADFLA- 101

Query: 92  KLVDATFAER------VFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRT 145
            L D     R      +F   +G  A EAA KLAR++      T +  ++A  N FHG T
Sbjct: 102 ALEDVILTPRDLDYRAMFTGPTGTNAVEAAIKLARKI------TGRELVIAFTNGFHGMT 155

Query: 146 LFTVNVGGQSKYSDGFGPKITGITHVPYN-------DLAA-LKAAVSDKT------CAVV 191
           L  +   G +    G G  +  ++H PY+       D A  L+  +SD +       A++
Sbjct: 156 LGALACTGNAAKRGGAGVPLNHVSHEPYDGYHGPGVDTAEQLERRLSDPSSGLDAPAAIL 215

Query: 192 LEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDIL 251
           +E +QGEGG+  A   +L+   ++   H AL++ D++Q G GR+G  F+++  G TPDI+
Sbjct: 216 VETVQGEGGLNAASPRWLRQIADIAKRHGALMIIDDIQAGCGRTGNFFSFEGMGFTPDIV 275

Query: 252 TSAKSLGG-GFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVI-DVINTPEVLN 309
           T AKSL G G P A  L   +L      G H  T+ GN  A   A A +    +      
Sbjct: 276 TMAKSLSGMGLPFALTLFRPEL-DQWSPGEHNGTFRGNNHAFVTATATLRHFWSDGNFQQ 334

Query: 310 GVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGK-AKDIFNAAEREGLMI 368
            +  +    + RL  +  ++GL   +RG G++ G    D   G+ A+ I  A   +GL+I
Sbjct: 335 DIARRGALLERRLAAMATEHGL--SIRGRGMMRGI---DVGSGEIAQTITAACFAQGLII 389

Query: 369 LQAG--PDVIRFAPSLVVEDADIDAGLDRFERA 399
             +G   ++++    LV++D+ + AGLD  E++
Sbjct: 390 ETSGAHDEIVKVLAPLVIDDSVLSAGLDILEQS 422


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: 446
Number of extensions: 29
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: 406
Length of database: 436
Length adjustment: 32
Effective length of query: 374
Effective length of database: 404
Effective search space:   151096
Effective search space used:   151096
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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