GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Dinoroseobacter shibae DFL-12

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 3607893 Dshi_1301 Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Dino:3607893
          Length = 661

 Score =  322 bits (825), Expect = 3e-92
 Identities = 183/452 (40%), Positives = 264/452 (58%), Gaps = 9/452 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F R+L+ANRGEIA RV+   + +G+  +AV+S+ D  A H   AD A  +G A   DSYL
Sbjct: 2   FERILIANRGEIACRVIDTCRRLGVQTVAVHSDVDAGARHVAMADMAVNLGGAAPRDSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
             E II AA     +AIHPGYGFLSEN +F EAV  AG+ FIGPS+  +R +  K   K 
Sbjct: 62  RGEAIIAAARATGAEAIHPGYGFLSENPDFVEAVAAAGLVFIGPSAAAIRAMGLKDAAKA 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           L   AGVP  PG  G           AE IGYP+++KA +GGGG G+ RV+  +      
Sbjct: 122 LMAEAGVPVVPGYQGADQDPARLAAEAEAIGYPVLIKAVAGGGGKGMRRVEGPEGFAGAL 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           E  +  A  AFG   + +EKY   PRHIE Q+ GD     V  +ER+C++QRR+QK+IEE
Sbjct: 182 EAARAEARGAFGNDHVLLEKYVATPRHIELQVFGDG-ARAVHLFERDCSLQRRHQKVIEE 240

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFE--TAFSDVSRD--FYFLELNKRLQVE 299
           AP+P +  E R +M    ++  + I Y   GT E     SD  R   F+F+E+N RLQVE
Sbjct: 241 APAPGMTPEMRAAMGAAAVRAAEAIGYAGAGTVEFIVDASDGLRPDRFWFMEMNTRLQVE 300

Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359
           HP TE +  +DLV  Q+++A+GE LP  QEDL+  +RG A E R+ AED    F  ++G 
Sbjct: 301 HPVTEAVTGVDLVAWQLRVASGEPLPARQEDLS--LRGHAFEARLYAEDVPKGFLPATGR 358

Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419
           +T+   P     R+++G+ +G  + P+YD +++KL+V+G +R+ A++   R LA  ++ G
Sbjct: 359 LTHLAFPA--DARIETGVRAGDEISPWYDPMIAKLVVHGPTRQSALRKLDRVLAGCEVAG 416

Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQKTD 451
             T +   + + +   F  G+  T  I ++ +
Sbjct: 417 SVTNLAFLRALARHGGFFAGEVDTGLIDREVE 448


Lambda     K      H
   0.317    0.135    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: 776
Number of extensions: 41
Number of successful extensions: 6
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: 509
Length of database: 661
Length adjustment: 36
Effective length of query: 473
Effective length of database: 625
Effective search space:   295625
Effective search space used:   295625
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 (21.6 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:

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