GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Synechococcus elongatus PCC 7942

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate Synpcc7942_1379 Synpcc7942_1379 acetyl-CoA carboxylase biotin carboxylase subunit

Query= BRENDA::Q9I299
         (655 letters)



>FitnessBrowser__SynE:Synpcc7942_1379
          Length = 453

 Score =  470 bits (1210), Expect = e-137
 Identities = 240/439 (54%), Positives = 311/439 (70%), Gaps = 1/439 (0%)

Query: 10  RLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRG 69
           ++L+ANRGEIA R++R+   LGIG++AVHS +DR+A HV  AD AV +G A  + SYL  
Sbjct: 5   KILIANRGEIALRILRTCEELGIGTIAVHSTVDRNALHVQLADEAVCIGEAASSKSYLNI 64

Query: 70  DRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALM 129
             IIAAAL   A AIHPGYGFL+ENA FA  C +  L F+GP   +I AMG KS AK  M
Sbjct: 65  PNIIAAALTRNASAIHPGYGFLAENARFAEICADHHLTFIGPSPDSIRAMGDKSTAKETM 124

Query: 130 EEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSS 189
           +  GVP +PG  G   D+++  + A  IGYPV++KA AGGGG+GM++V   A+L +   +
Sbjct: 125 QRVGVPTIPGSDGLLTDVDSAAKVAAEIGYPVMIKATAGGGGRGMRLVREPADLEKLFLA 184

Query: 190 AQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAP 249
           AQ EA+AAFG+  + +EK++ +PRHVE Q+ AD +G+ ++L ERDCSIQRRHQK++EEAP
Sbjct: 185 AQGEAEAAFGNPGLYLEKFIDRPRHVEFQILADAYGNVVHLGERDCSIQRRHQKLLEEAP 244

Query: 250 APGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTEAI 309
           +P L A+LR+ MG+AAV+ AQAIGY+GAGTVEFL+D  G F+FMEMNTR+QVEHPVTE I
Sbjct: 245 SPALSADLRQKMGDAAVKVAQAIGYIGAGTVEFLVDATGNFYFMEMNTRIQVEHPVTEMI 304

Query: 310 TGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAAA 369
           TGLDL+A QIR+A+GEAL   Q  + L GHAIE R+ AEDPE +F P  GR+  Y     
Sbjct: 305 TGLDLIAEQIRIAQGEALRFRQADIQLRGHAIECRINAEDPEYNFRPNPGRITGYL-PPG 363

Query: 370 GPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAFL 429
           GPG RVDS V    E+ P+YD ++ KLI WG TREEA  R+   L E ++ GL T L+F 
Sbjct: 364 GPGVRVDSHVYTDYEIPPYYDSLIGKLIVWGATREEAIARMQRALRECAITGLPTTLSFH 423

Query: 430 RRILGHPAFAAAELDTGFI 448
           + +L  P F   EL T F+
Sbjct: 424 QLMLQMPEFLRGELYTNFV 442


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: 26
Number of successful extensions: 2
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: 453
Length adjustment: 35
Effective length of query: 620
Effective length of database: 418
Effective search space:   259160
Effective search space used:   259160
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:

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