GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Amantichitinum ursilacus IGB-41

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 WP_053939334.1 WG78_RS18565 urea carboxylase

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



>NCBI__GCF_001294205.1:WP_053939334.1
          Length = 1216

 Score =  352 bits (903), Expect = e-101
 Identities = 189/445 (42%), Positives = 277/445 (62%), Gaps = 5/445 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+ VL+ANRGEIA R ++ +K +G+ ++AV+S+AD+ + H   AD A  +G     DSYL
Sbjct: 2   FNTVLIANRGEIACRAIRTLKHLGVVSVAVFSDADRNSAHVAQADVAIALGGDRPADSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
            I+ IIDA ++    A+ PGYGFLSE+AEFA A +  GI FIGP++  M++   K   + 
Sbjct: 62  RIDKIIDACKQTGAQAVFPGYGFLSESAEFAAACDANGIVFIGPTALQMQEFGLKHRARE 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           LA  AGVPT PGS G + S+ +AL+ A KIGYP+M+K+ +GGGG+G+TR ++ ++L   +
Sbjct: 122 LAAQAGVPTTPGS-GLLASVADALEQAGKIGYPVMLKSTAGGGGIGLTRCNSAEELAAAF 180

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           +R +R+  Q F  +  F+E++    RHIE Q+ GD  G      ER+C+IQRRNQK+IEE
Sbjct: 181 DRVQRMGEQFFRDSGAFVERFVDQARHIEVQIFGDGKGQVAALGERDCSIQRRNQKVIEE 240

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
            P+P L    R ++       G+ +NY + GT E  +     +FYFLE+N RLQVEHP T
Sbjct: 241 TPAPNLPAATRAALLASAKALGESVNYRSAGTVEYVYDSARDEFYFLEVNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E +  +DLV+  +++AAG+ L +  + LN   +G AIE R+ AED +  F  S G +T  
Sbjct: 301 ESVTGLDLVECMLRVAAGDALDW--DALNAAPQGAAIEVRLYAEDPVKQFQPSPGLLTEV 358

Query: 364 REPTGP--GVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIK 421
           R P      VRVD  +++G+ VP  YD L++KLIV G  RE A+    +ALA   + GI 
Sbjct: 359 RFPESDIVPVRVDGWVQTGTEVPSLYDPLLAKLIVKGADREQALDNLQKALAHTALHGIA 418

Query: 422 TTIELYKWIMQDPDFQEGKFSTSYI 446
           T ++  + I+    F  GK ST ++
Sbjct: 419 TNLDYLRQIIASEAFYSGKVSTRFL 443


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: 1279
Number of extensions: 55
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: 509
Length of database: 1216
Length adjustment: 41
Effective length of query: 468
Effective length of database: 1175
Effective search space:   549900
Effective search space used:   549900
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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