GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Paucidesulfovibrio gracilis DSM 16080

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_078718056.1 B5D49_RS12550 pyruvate carboxylase

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



>NCBI__GCF_900167125.1:WP_078718056.1
          Length = 1233

 Score =  305 bits (781), Expect = 6e-87
 Identities = 185/474 (39%), Positives = 276/474 (58%), Gaps = 11/474 (2%)

Query: 7   VLVANRGEIATRVLKAIKEMGMT-AIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           +LVANRG  A R+ + I EM    ++   ++ DK +  T  A+E   +G  P   +YL+I
Sbjct: 18  ILVANRGIPARRICRTISEMSEAISVMTATDVDKTSPATSGANELMLLGDDPR--AYLDI 75

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
           + II  A+   V AIHPG+GF +E+  F E  ++AGI FIGP ++ MR + +K+  +RLA
Sbjct: 76  DTIIQRAKDRGVIAIHPGWGFAAEDESFPEKCKEAGIIFIGPPTDAMRTLGNKVAVRRLA 135

Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185
              GVP  PGS+  V  I +A ++A++IG PIM+KA  GGGG GI  V ++DQL   + +
Sbjct: 136 QEIGVPVVPGSEEAV-DIPKAREIAKQIGLPIMLKAEGGGGGRGIYEVYSEDQLEKAFHK 194

Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245
              LA  +FG   L+IEK   + RHIE Q+I D++GN     ER+C++QR +QKLIE  P
Sbjct: 195 ASALAQASFGNPRLYIEKLLTSVRHIEIQVIADQHGNVFAFDERDCSVQRNHQKLIEITP 254

Query: 246 SPALKM--EERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           SP  +M  E RE + E      K + Y+++ T E    +     Y +E+N RLQVEH  T
Sbjct: 255 SPWPQMTPELREQLKEYSRNLVKAVGYYSVCTVEFLVEEDGTP-YLIEVNTRLQVEHGIT 313

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E  + IDLV+ Q+ +A G  L F++E  N +    A++ RIN ED  N+F+ ++  +  Y
Sbjct: 314 ECRYGIDLVEEQVAIAFGSKLRFTEE--NCKPFQHALQVRINFEDPQNSFSPNAARIERY 371

Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423
             P G GVR+DS I  G   P  YDS  + LI YG S E  +    RAL +Y IGG+KTT
Sbjct: 372 FAPGGQGVRLDSCIGEGYTFPSQYDSAAALLITYGRSWEKTVLLMRRALREYVIGGVKTT 431

Query: 424 IELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEI--KAAIAAEIQSRG 475
           I  ++ +++ PDF    ++T ++    ++ + Y  E ++      + AEI ++G
Sbjct: 432 IPFHRQVLKHPDFFYANYNTKFVDMHKNELLAYSDEAKDSFRLCRLIAEISAKG 485


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: 1294
Number of extensions: 65
Number of successful extensions: 6
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: 1233
Length adjustment: 41
Effective length of query: 468
Effective length of database: 1192
Effective search space:   557856
Effective search space used:   557856
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 Apr 09 2024. 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