GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Phaeobacter inhibens BS107

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 GFF1244 PGA1_c12600 biotin carboxylase AccA

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



>lcl|FitnessBrowser__Phaeo:GFF1244 PGA1_c12600 biotin carboxylase
           AccA
          Length = 450

 Score =  374 bits (960), Expect = e-108
 Identities = 197/443 (44%), Positives = 277/443 (62%), Gaps = 5/443 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F ++L+ANRGEIA RV++A +EMG+ ++AV+S AD  A+H + ADE+  IG      SYL
Sbjct: 2   FDKILIANRGEIALRVIRACREMGIQSVAVHSTADADAMHVRMADESVCIGPPSGTHSYL 61

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

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
                GVP  PGSDG V  ++ A K+ E IGYP+++KA +GGGG G+        +   +
Sbjct: 122 TMKDLGVPCVPGSDGGVPDLETAKKIGEDIGYPVIIKATAGGGGRGMKVAKTAADMEQAF 181

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

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           AP P +  EER  + +   +    INY   GT E  +     +FYF+E+N RLQVEHP T
Sbjct: 242 APGPCITPEERARIGKTCAEAVAKINYIGAGTIEFLYE--KGEFYFIEMNTRLQVEHPVT 299

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E IF +DLV+ QI++A G  + FSQ+DL   + G +IE RINAE  L NF+   G +T Y
Sbjct: 300 ESIFGVDLVREQIRVAEGLPMSFSQDDL--EINGHSIEVRINAE-KLPNFSPCPGRITQY 356

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

Query: 424 IELYKWIMQDPDFQEGKFSTSYI 446
           + L+  ++++ D + G+++  ++
Sbjct: 417 VPLFHALLEEKDIRTGEYNIHWL 439


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: 545
Number of extensions: 24
Number of successful extensions: 5
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: 450
Length adjustment: 34
Effective length of query: 475
Effective length of database: 416
Effective search space:   197600
Effective search space used:   197600
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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