GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Sphingobium czechense LL01

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_066601311.1 V473_RS05465 CoA transferase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>NCBI__GCF_001046645.1:WP_066601311.1
          Length = 395

 Score =  240 bits (612), Expect = 6e-68
 Identities = 153/406 (37%), Positives = 219/406 (53%), Gaps = 21/406 (5%)

Query: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60
           +GAL  +RVLD + V+AGP+A ++LADLGA+VIKVE    GD  RA  P        +  
Sbjct: 10  VGALDGVRVLDFTSVMAGPFATRMLADLGAEVIKVESL-EGDQVRARPP--------KRD 60

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
             +AY+ + N  KQS+  +   PE   L+++L A  DIL+ENF+ G +A +GLD+ +L+ 
Sbjct: 61  GFSAYFGNLNAGKQSIACNLKSPEIIALIKDLIATCDILVENFRPGVMARFGLDFAALRE 120

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
            NP+LIYCSI+G+GQTGP A    Y  +I    G   +  R + D    P   GV + D+
Sbjct: 121 ANPRLIYCSISGYGQTGPKALSPAYAPVIHAASGFDMVNLRYQ-DGADRPATSGVFIADV 179

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
           L G ++  AI AAL  R+  G GQHID+++L+  V  L  +       G+A + L     
Sbjct: 180 LGGTHAFGAIQAALYQREKTGAGQHIDLSMLEAMVGMLVFETQEAQFPGDARRPL----- 234

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
               Y    T DG  ++   +   F +  +  G P+W DDPRF TN  R AN A L+ L 
Sbjct: 235 ----YTPLKTNDGFIMVAPTSPRNFEQLTDAVGHPEWRDDPRFLTNADRNANWATLLALT 290

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
              T  ++  E    L + GVPCG   ++ ++  DPQ+ +RG   E+    AG       
Sbjct: 291 ETWTRERSAEEAEAILSRHGVPCGRYREIDELLDDPQLASRGAFAEISD-GAGSFKVPNP 349

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           P R+S + VE RN    LGE   ++L + LG+DE+AV A R  G L
Sbjct: 350 PFRMSGSRVEARNHVARLGEEGADILTK-LGVDESAVAALRARGDL 394


Lambda     K      H
   0.319    0.137    0.408 

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: 445
Number of extensions: 19
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: 395
Length adjustment: 31
Effective length of query: 375
Effective length of database: 364
Effective search space:   136500
Effective search space used:   136500
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 (21.7 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