GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuB in Dechlorosoma suillum PS

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate Dsui_0389 Dsui_0389 acetyl-CoA carboxylase, biotin carboxylase subunit

Query= BRENDA::Q9I299
         (655 letters)



>lcl|FitnessBrowser__PS:Dsui_0389 Dsui_0389 acetyl-CoA carboxylase,
           biotin carboxylase subunit
          Length = 455

 Score =  412 bits (1059), Expect = e-119
 Identities = 221/431 (51%), Positives = 291/431 (67%), Gaps = 4/431 (0%)

Query: 9   QRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLR 68
           +++L+ANRGEIA RV R+ R LGI +V VHS+ DR A++V  AD +V +G A  A SYL 
Sbjct: 3   EKILIANRGEIALRVQRACRELGIKTVVVHSEADREAKYVKLADESVCIGPASSALSYLN 62

Query: 69  GDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKAL 128
              II+AA  + AQAIHPGYGFLSENADFA   E +G +F+GP A  I  MG K +AK  
Sbjct: 63  IPAIISAAEVTDAQAIHPGYGFLSENADFAERVESSGFVFIGPRAETIRLMGDKVSAKDA 122

Query: 129 MEEAGVPLVPGYHGEA-QDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187
           M+ AGVP VPG  G   +D +   +    +GYPV++KAA GGGG+GM+VV  EA L  A+
Sbjct: 123 MKAAGVPCVPGSDGALPEDPKEIIKIGRAVGYPVIIKAAGGGGGRGMRVVHTEAALINAV 182

Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247
           +  ++EA+ AFG+  + +EK+L  PRHVEIQV AD   + +YL ERDCS+QRRHQKV+EE
Sbjct: 183 AMTRQEAQTAFGNPMVYMEKFLENPRHVEIQVLADEFKNAVYLGERDCSMQRRHQKVIEE 242

Query: 248 APAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTE 307
           APAPG+ A L   +GE    A + IGY GAGT EFL  E G+F+F+EMNTR+QVEHPVTE
Sbjct: 243 APAPGIPARLIARVGERCAEACRRIGYRGAGTFEFLY-ENGEFYFIEMNTRVQVEHPVTE 301

Query: 308 AITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREA 367
            ITG+D+V  QIR+A GE L   Q  +   GHAIE R+ AEDP   F+P+ G +  +   
Sbjct: 302 LITGIDIVQEQIRIAAGEKLRFKQRDIQFRGHAIECRVNAEDP-FTFVPSPGTISWW-HP 359

Query: 368 AAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLA 427
             GPG RVDS    G +V P YD M+ K+I +G+TRE+A +R+   L+ET V G++TN+ 
Sbjct: 360 PGGPGVRVDSHAYSGYKVPPHYDSMIGKIITFGDTREQAIRRMRIALSETVVQGIKTNIP 419

Query: 428 FLRRILGHPAF 438
             + ++    F
Sbjct: 420 LHQELMQDARF 430


Lambda     K      H
   0.319    0.135    0.397 

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: 714
Number of extensions: 22
Number of successful extensions: 4
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: 655
Length of database: 455
Length adjustment: 35
Effective length of query: 620
Effective length of database: 420
Effective search space:   260400
Effective search space used:   260400
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: 52 (24.6 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 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