GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Marinobacter adhaerens HP15

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF2594 HP15_2538 acetyl/propionyl-CoA carboxylase beta subunit

Query= metacyc::MONOMER-17283
         (535 letters)



>FitnessBrowser__Marino:GFF2594
          Length = 538

 Score =  424 bits (1091), Expect = e-123
 Identities = 227/545 (41%), Positives = 326/545 (59%), Gaps = 17/545 (3%)

Query: 1   MSIIHSHIQPNSPDFQAN---FAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVR 57
           M ++ S +   S DF+ N      H +   D+ +++  + +      R +  +RGKL  R
Sbjct: 1   MQVLESTVSSTSEDFRTNAEAMDAHITTFRDVEQKVLDLAEAA----REKFTKRGKLLPR 56

Query: 58  DRIDTLIDPDSSFLEIGALAAYNVYDEE---VPAAGIVCGIGRVAGRPVMIIANDATVKG 114
           DRI+ L+D  + FLE+ +LA Y ++D++   +   GI+ GIG V+G   +++A+++ +KG
Sbjct: 57  DRINRLLDRGTPFLELCSLAGYKMHDDKDGSLAGGGIIAGIGYVSGIRCLVVASNSAIKG 116

Query: 115 GTYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMS 174
           GT  P  + K LR Q+IA EN+LP + L +SGGA L   +++F       R F NQA+MS
Sbjct: 117 GTITPAGLDKTLRLQQIAMENKLPVVSLSESGGANLNYATDIFVLG---ARGFANQARMS 173

Query: 175 AEGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGG 234
           A GIPQ+  V G+ TAGGAY P +SD V++V+    +FL GPPL+KAATGE  T EELGG
Sbjct: 174 AAGIPQVTVVHGNATAGGAYQPGLSDYVIVVREQAKMFLAGPPLLKAATGEVATDEELGG 233

Query: 235 ADVHTRISGVADYFANDDREALAIVRDIVAHLGPRQRAN-WELRDPEPPRYDPREIYGIL 293
           A++H  ++G A+Y A DD + +   R+I+  L   ++   W     E P Y   E+ G++
Sbjct: 234 AEMHATVAGTAEYLAEDDADGIRQARNILEALPWNEQLQPWRELQWEEPLYPADELLGVI 293

Query: 294 PRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESA 353
           P D ++ YDVRE++ARI DGS+  +FK  +    VCG   IEG  VGI+ NNG +    +
Sbjct: 294 PADSKKPYDVREILARIADGSKFMDFKNEFDDQTVCGTIRIEGHSVGIIGNNGPITPAGS 353

Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413
            K A FI+LC     PL+FL N TGFMVG   E  GI K G+K++ AV+   VPK  ++I
Sbjct: 354 AKAAQFIQLCDQAGTPLLFLHNTTGFMVGTHSEQNGIIKHGSKMIQAVANCRVPKVAIVI 413

Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473
           GGS+GAGNY MCGR   PR ++ WPN+R +VMG  QA  V+  +  D  R  G +  P+ 
Sbjct: 414 GGSYGAGNYAMCGRGLDPRFIFAWPNSRTAVMGPAQAGKVMRIVAEDKQRRGGMEPDPKT 473

Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPTRF 530
            +        K E+     + +ARLWDDG+IDP +TRRVLAL L    EA    ++P  F
Sbjct: 474 LDFLEQATAKKLEEGSTALFGTARLWDDGLIDPRDTRRVLALVLDVCREAEARQLRPNTF 533

Query: 531 GVFRM 535
           GV R+
Sbjct: 534 GVARL 538


Lambda     K      H
   0.322    0.139    0.423 

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: 768
Number of extensions: 43
Number of successful extensions: 5
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: 535
Length of database: 538
Length adjustment: 35
Effective length of query: 500
Effective length of database: 503
Effective search space:   251500
Effective search space used:   251500
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 (21.9 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