GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Shewanella oneidensis MR-1

Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate 200026 SO0840 acetyl-CoA carboxylase multifunctional enzyme accADC, carboxyl transferase subunit alpha/carboxyl transferase subunit beta/biotin carboxylase (NCBI ptt file)

Query= SwissProt::P0DTA4
         (730 letters)



>FitnessBrowser__MR1:200026
          Length = 1517

 Score =  310 bits (795), Expect = 3e-88
 Identities = 174/453 (38%), Positives = 273/453 (60%), Gaps = 12/453 (2%)

Query: 61   KTFDKILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTM---ADEAVCVGPAPT 117
            K  +K+L+  RG  A ++I+      I  V V SD D ++V   M   +D+ VC+G   +
Sbjct: 938  KPINKVLVHARGCTAVKLIRKAHDNNINVVLVASDPDMTAVPADMLKESDKLVCLGGNTS 997

Query: 118  SKSYLNMDAIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDK 177
             +SYLN  ++++     +  A+HPG GFLSE+ +FA      GV F+GP  H++  MG+K
Sbjct: 998  DESYLNAYSVLKVAEYEQVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNK 1057

Query: 178  IESKLLAKKAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEE 237
              +   ++   V  +PG  G++ +A++AV +A EIGYPV++KA  GGGGKG+++    E+
Sbjct: 1058 SNAIKTSQAQNVPVVPGSHGILTNAEQAVNVASEIGYPVLLKAVQGGGGKGIQVVKRPED 1117

Query: 238  TRDGFRFSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQ 297
                F+ ++ EAA++FG+  L +EK++ + RHIE+Q+L DK G+A  L  R+CS+QR NQ
Sbjct: 1118 MIGLFQKTATEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGHAKVLGLRDCSVQRNNQ 1177

Query: 298  KVVEEAPSIFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKKN-FYFLEMNTRLQV 356
            KVVEE+ S  L  E ++ +     AL  A +Y  AGTVEF+ +   N  YF+EMNTRLQV
Sbjct: 1178 KVVEESGSTMLPDELKKQVLAYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQV 1237

Query: 357  EHPVTECITGLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAED-PYKSFG----L 411
            EHPVTE  +G+D+V     +A G  + H +      G+A+E RV AE     S G    +
Sbjct: 1238 EHPVTEATSGIDIVSAQFDIAAGRSIEHLEP--KEIGYAMEVRVTAEKAALDSHGVLQLI 1295

Query: 412  PSIGRLSQYQEPIHLPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALD 471
            P+ G++++   P H P V + S   PG ++S YYD +I+++I  G NR + + ++   LD
Sbjct: 1296 PNPGKITECVFPDH-PDVEIISIAAPGKEVSPYYDSLIAQVIMRGENREDVIAKLHAYLD 1354

Query: 472  NYVIRGVTHNIALLREVIINSRFVEGDINTKFL 504
            + V++G+  NI LL+ ++ +  F EG  +T +L
Sbjct: 1355 SVVLKGIATNIPLLKLILSDGTFKEGVYDTNYL 1387



 Score = 28.9 bits (63), Expect = 0.002
 Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 15/87 (17%)

Query: 653  LEKAAEDTSSILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAG-------- 704
            L+  A+       SP PG      VK GD+V   Q + + EAMKM + +           
Sbjct: 1425 LKVLAQGAGIFYTSPAPGE--PDFVKEGDIVTAEQTLALTEAMKMFSQVNLAGFNRQGAV 1482

Query: 705  -----KTGKVKSVHCKAGDTVGEGDLL 726
                 K  +++ +    G  V +GDLL
Sbjct: 1483 LYPEDKKYRIERILNSNGQQVSQGDLL 1509


Lambda     K      H
   0.318    0.134    0.385 

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: 2148
Number of extensions: 82
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 730
Length of database: 1517
Length adjustment: 45
Effective length of query: 685
Effective length of database: 1472
Effective search space:  1008320
Effective search space used:  1008320
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: 58 (26.9 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 (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