GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Pseudomonas stutzeri RCH2

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 GFF987 Psest_1019 acetyl-CoA carboxylase, biotin carboxylase subunit

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



>lcl|FitnessBrowser__psRCH2:GFF987 Psest_1019 acetyl-CoA
           carboxylase, biotin carboxylase subunit
          Length = 449

 Score =  382 bits (982), Expect = e-110
 Identities = 202/445 (45%), Positives = 291/445 (65%), Gaps = 6/445 (1%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           +VL+ANRGEIA RVL+A KE+G+  +AV+S AD+  +H   ADE+  IG A +  SYL+I
Sbjct: 4   KVLIANRGEIALRVLRACKELGIKTVAVHSTADRDLMHVSLADESVCIGPAASAKSYLSI 63

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
             +I AAE    D IHPGYGFL+ENA+FAE VEK+G TFIGP+++V+R + DK+  K   
Sbjct: 64  PALIAAAEVTGADGIHPGYGFLAENADFAEQVEKSGFTFIGPTADVIRLMGDKVSAKDAM 123

Query: 126 NMAGVPTAPGSDGPVTSID-EALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWE 184
             AGVPT PGSDGP+   + EAL++A ++GYP+++KAA GGGG G+  V  ++ L+   +
Sbjct: 124 KQAGVPTVPGSDGPLPEDEKEALRIAREVGYPVIIKAAGGGGGRGMRVVHKEEDLIASAK 183

Query: 185 RNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEA 244
             +  A  AFG   +++EK+  NPRH+E Q++ D  GN +   +R+C++QRR+QK+IEEA
Sbjct: 184 LTRNEAGAAFGNPMVYLEKFLTNPRHVEIQVLADGQGNAIHLGDRDCSLQRRHQKVIEEA 243

Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304
           P+P +  E R  +    +K    I Y   GTFE  + D   +FYF+E+N R+QVEHP TE
Sbjct: 244 PAPLIDEEARRKVQARCVKACIDIGYRGAGTFEFLYED--GNFYFIEMNTRVQVEHPVTE 301

Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364
           ++  ID+VK  + +  G+ L   QED+   +RG A+E RINAED    F  S G V ++ 
Sbjct: 302 MVTGIDIVKEMLLIGGGQKLSIKQEDV--VIRGHAVECRINAEDP-RTFMPSPGKVKHFH 358

Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424
            P G GVRVDS +  G  VPP+YDSL+ KLI +G +R+ A+     AL +  + GIKT  
Sbjct: 359 APGGNGVRVDSHLYDGYSVPPHYDSLIGKLITFGANRDEAMGRMRNALDELIVDGIKTNA 418

Query: 425 ELYKWIMQDPDFQEGKFSTSYISQK 449
            L++ +++DP F +G  +  Y+ +K
Sbjct: 419 PLHRDLVRDPGFCKGGVNIHYLEKK 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: 562
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: 449
Length adjustment: 34
Effective length of query: 475
Effective length of database: 415
Effective search space:   197125
Effective search space used:   197125
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 paper from 2022 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