GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS02215 CA265_RS02215 acetyl-CoA carboxylase biotin carboxylase subunit

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



>FitnessBrowser__Pedo557:CA265_RS02215
          Length = 503

 Score =  419 bits (1076), Expect = e-121
 Identities = 222/493 (45%), Positives = 315/493 (63%), Gaps = 5/493 (1%)

Query: 3   PFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSY 62
           P S++LVANRGEIA R++++ KEMG+  +AV+SEAD+ A+H +YADEA  IG AP+  SY
Sbjct: 10  PISKLLVANRGEIALRIMRSAKEMGIKTVAVFSEADRNALHVRYADEAVCIGPAPSNQSY 69

Query: 63  LNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGK 122
           L  E II A +    +AIHPGYGFLSENA FA+ V  AG+  +GPS + M  + +KL  K
Sbjct: 70  LVGEKIIGACKLTGAEAIHPGYGFLSENAGFAQMVADAGLILVGPSPQAMETMGNKLSAK 129

Query: 123 RLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182
             A    +P  PG++  +  ++EA + A ++G+PI++KAA+GGGG G+  V+  +   + 
Sbjct: 130 AAALKYNIPMVPGTEEAIQDVNEAKQRAIEVGFPILIKAAAGGGGKGMRIVERAEDFEEQ 189

Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242
            +     A  AFG   +FIE+Y  +PRHIE Q++GD +GN V  +EREC++QRR+QK+IE
Sbjct: 190 MQLAVSEATSAFGDGAVFIERYVTSPRHIEIQVLGDNHGNIVHLFERECSVQRRHQKVIE 249

Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302
           EAPS  L  E R+ M +  +   + +NY   GT E    D + DF+FLE+N RLQVEHP 
Sbjct: 250 EAPSSVLTEEIRQRMGKCAVDVARSVNYTGAGTVEFIL-DENLDFFFLEMNTRLQVEHPV 308

Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362
           TELI  IDLVK Q+K+A+GE L FSQEDL  ++ G A+E R+ AED  NNF    G +  
Sbjct: 309 TELITGIDLVKEQLKIASGEKLSFSQEDL--KISGHAVELRVYAEDPANNFLPDIGTLQT 366

Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
           Y  P G GVRVD G E G  +P YYD +++KLI YG+ RE AI+  +RA+ +Y I GI+T
Sbjct: 367 YNTPKGNGVRVDDGFEQGMEIPIYYDPMIAKLITYGKDREEAIERMVRAIEEYDITGIET 426

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSST 482
           T+   K++MQ   F+ G F T ++ +      + L+ Q+E +A IAA I ++   +    
Sbjct: 427 TLGFGKFVMQHEAFKTGNFDTHFVGKYFKP--ESLKVQDETEALIAAVIAAKLFDKKEVK 484

Query: 483 DNKGKAQSKSGWK 495
                 ++ S W+
Sbjct: 485 LGDAAIKNSSDWR 497


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: 592
Number of extensions: 28
Number of successful extensions: 3
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: 503
Length adjustment: 34
Effective length of query: 475
Effective length of database: 469
Effective search space:   222775
Effective search space used:   222775
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: 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