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 3607987 Dshi_1395 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)

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



>FitnessBrowser__Dino:3607987
          Length = 448

 Score =  377 bits (967), Expect = e-109
 Identities = 201/445 (45%), Positives = 284/445 (63%), Gaps = 5/445 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           FS++L+ANRGEIA RV++A +E+G+ ++AV+S AD  A+H + ADEA  IG  P+  SYL
Sbjct: 2   FSKILIANRGEIALRVIRACRELGIQSVAVHSTADTDAMHVRMADEAVCIGPPPSPQSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           +I  II A E    +AIHPGYGFLSENA F + V+  G+TFIGP++E +R + DK+  K 
Sbjct: 62  SIPAIISACEITGAEAIHPGYGFLSENANFVQIVQDHGLTFIGPTAEHIRVMGDKITAKE 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
                GVP  PGSDG V  ++ A ++A +IGYP++VKA +GGGG G+      + L + +
Sbjct: 122 TMKNLGVPCVPGSDGGVPDLETARRVAGEIGYPVIVKATAGGGGRGMKLAKTAEDLDEAF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           +  +     AFG  D+++EKY   PRHIE Q+ GD  G  V   ER+C++QRR+QK+ EE
Sbjct: 182 QTARSEGKAAFGNPDVYLEKYLSTPRHIEVQVFGDGKGGAVHLGERDCSLQRRHQKVFEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           APSP +  E R  + +   +    I+Y   GT E  +   + +FYF+E+N RLQVEHP T
Sbjct: 242 APSPVIDAETRARIGKTCAEAVARIDYAGAGTIEFLYE--NGEFYFIEMNTRLQVEHPVT 299

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E IF +DLVK QI++AAG  + F QE+L  +VRG AIE RINAE  +  FT   G VT +
Sbjct: 300 EAIFGVDLVKEQIRVAAGYPMTFKQENL--QVRGHAIEVRINAE-KVPAFTPCPGMVTTF 356

Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423
             P G GVR+DS +  G  +PPYYDSL+ KLIV  + R  A+    RAL +  + GI TT
Sbjct: 357 HTPGGLGVRMDSALYGGYSIPPYYDSLIGKLIVLAQDRPAALARLNRALGELIVDGIDTT 416

Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448
           + L+  ++ +   Q G ++  ++ +
Sbjct: 417 VPLFHALLAEEAIQTGDYTIHWLEE 441


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: 582
Number of extensions: 20
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: 448
Length adjustment: 34
Effective length of query: 475
Effective length of database: 414
Effective search space:   196650
Effective search space used:   196650
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: 51 (24.3 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