GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdG in Burkholderia phytofirmans PsJN

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate BPHYT_RS13985 BPHYT_RS13985 CoA transferase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS13985 BPHYT_RS13985 CoA
           transferase
          Length = 406

 Score =  528 bits (1361), Expect = e-155
 Identities = 252/406 (62%), Positives = 306/406 (75%)

Query: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60
           MGALSH+RVLDL+RVLAGPW  Q LAD GADVIK+ERP  GDDTR WGPP+LK   GE+T
Sbjct: 1   MGALSHIRVLDLTRVLAGPWCAQTLADFGADVIKIERPEVGDDTRHWGPPYLKTPEGEDT 60

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
            EAAYYL+ANRNK+SVT+D   PEGQR++RELAA+SD+++EN+KVG L  YGLDY SLK 
Sbjct: 61  REAAYYLAANRNKRSVTVDIASPEGQRIIRELAAQSDVVLENYKVGQLKKYGLDYASLKE 120

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
           + P ++YCS+TGFGQTGPYA+RAGYDF++QG+GG MS+TG  +G  G GP K GVA+ D+
Sbjct: 121 VKPDIVYCSVTGFGQTGPYAQRAGYDFIVQGIGGFMSITGERDGQPGGGPQKAGVAIADL 180

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
           +TG+YST A+L AL HRD  G GQ+IDMALLDVQVA LAN   NYL +G  P R GNAHP
Sbjct: 181 MTGMYSTIAVLTALTHRDRTGEGQYIDMALLDVQVAMLANMNSNYLASGQPPVRWGNAHP 240

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
           NIVPYQ F T+DG  I+ VGNDGQFRKF E  G+P+ ADD RFATN  RV NR VL+P++
Sbjct: 241 NIVPYQTFQTSDGWIIVAVGNDGQFRKFIEAGGRPELADDERFATNPARVRNRDVLVPIL 300

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
            +    +   +W+  LE AGVPCGPINDL +VF + QV ARGL ++LPH   G V  V +
Sbjct: 301 AEMVRLQGKQQWIAALEAAGVPCGPINDLGEVFENEQVVARGLQVDLPHPSGGTVKLVRN 360

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           PI ++ TP E    PP LGEHT  +L+ VLG DEA + A R   V+
Sbjct: 361 PINMTGTPPEALAHPPTLGEHTESILRDVLGYDEATIAALRSQSVI 406


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: 619
Number of extensions: 17
Number of successful extensions: 1
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: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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