GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuB in Pedobacter sp. GW460-11-11-14-LB5

Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate CA265_RS18365 CA265_RS18365 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::Q96RQ3
         (725 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS18365 CA265_RS18365 acetyl-CoA
           carboxylase biotin carboxylase subunit
          Length = 446

 Score =  421 bits (1082), Expect = e-122
 Identities = 211/439 (48%), Positives = 297/439 (67%), Gaps = 3/439 (0%)

Query: 51  KVLIANRGEIACRVMRTAKKLGVQTVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLSM 110
           K+LIANRGEIA R++RT K++G++TVAVYS ADR S+HV  ADEA  IGP PS+ SYL++
Sbjct: 4   KILIANRGEIALRIIRTCKEMGIKTVAVYSTADRESLHVRFADEAVCIGPPPSKDSYLNI 63

Query: 111 EKIIQVAKTSAAQAIHPGCGFLSENMEFAELCKQEGIIFIGPPPSAIRDMGIKSTSKSIM 170
             II  A+ + A AIHPG GFLSEN +F+ +C++  I FIG  P  I  MG K+++K  M
Sbjct: 64  PNIISAAELTNADAIHPGYGFLSENAKFSNICREYNIKFIGATPEQINGMGDKASAKETM 123

Query: 171 AAAGVPVVEGYHGEDQSDQCLKEHARRIGYPVMIKAVRGGGGKGMRIVRSEQEFQEQLES 230
             AGVP + G  G   S +     A  +GYPV++KA  GGGG+GMR+V  +++F+   +S
Sbjct: 124 KIAGVPTIPGSEGLLTSVKEGIAIANEMGYPVILKATAGGGGRGMRVVWKDEDFENAWDS 183

Query: 231 ARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAP 290
           AR+E+  +F +D + +EK+++ PRH+E+Q+ GD  G A +L ERDCS+QRRHQK++EE+P
Sbjct: 184 ARQESGAAFGNDGLYLEKYIEDPRHIEIQIIGDQFGKACHLSERDCSIQRRHQKLVEESP 243

Query: 291 APGIKSEVRKKLGEAAVRAAKAVNYVGAGTVEFIMDSKHNFCFMEMNTRLQVEHPVTEMI 350
           +P +  E+R ++GEAA++ A AVNY GAGT+EF++D   NF FMEMNTR+QVEHPVTE +
Sbjct: 244 SPFMTDELRVRMGEAAIKGAMAVNYEGAGTIEFLVDKHRNFYFMEMNTRIQVEHPVTEEV 303

Query: 351 TGTDLVEWQLRIAAGEKIPLSQEEITLQGHAFEARIYAEDPSNNFMPVAGPLVHLSTPRA 410
              DL++ Q+++AAG  IP+S +      HA E RI AEDP+NNF P  G + +  +P  
Sbjct: 304 INFDLIKEQIKVAAG--IPISGKNYFPDMHAIECRINAEDPANNFRPSPGKITNFHSP-G 360

Query: 411 DPSTRIETGVRQGDEVSVHYDPMIAKLVVWAADRQAALTKLRYSLRQYNIVGLHTNIDFL 470
               R++T V  G  +  +YD MIAKL+  A  R+ A+  +  +L ++ I G+ T I F 
Sbjct: 361 GHGVRVDTHVYAGYSIPSNYDSMIAKLICVAQTREEAICTMERALGEFVIEGVKTTIPFH 420

Query: 471 LNLSGHPEFEAGNVHTDFI 489
           L L   P F AGN  T F+
Sbjct: 421 LQLMKDPNFRAGNFTTKFM 439


Lambda     K      H
   0.317    0.131    0.377 

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: 742
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: 725
Length of database: 446
Length adjustment: 36
Effective length of query: 689
Effective length of database: 410
Effective search space:   282490
Effective search space used:   282490
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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