Alignments for a candidate for pccA in Halioglobus japonicus S1-36

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Halioglobus japonicus S1-36

Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate WP_084200978.1 C0029_RS16990 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= BRENDA::Q19842
         (724 letters)



>NCBI__GCF_002869505.1:WP_084200978.1
          Length = 664

 Score =  492 bits (1266), Expect = e-143
 Identities = 287/673 (42%), Positives = 397/673 (58%), Gaps = 17/673 (2%)

Query: 49  FDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYL 108
           F+KILIANRGEIACRVIKTAR MGI TVAV+SD DS +LHV MADEA+ +G +P   SYL
Sbjct: 2   FNKILIANRGEIACRVIKTAREMGIATVAVYSDADSQALHVHMADEAIHIGPSPARDSYL 61

Query: 109 RADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKK 168
            A+RIL A   T A A+HPGYGFLSEN  FA    +AG  FIGP + AI  MG K  +K+
Sbjct: 62  LAERILDAAVTTNADAIHPGYGFLSENAGFAQACAEAGVVFIGPPTAAIEAMGSKSAAKR 121

Query: 169 IATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGY 228
           I   A V ++PGY G+  D  +  + + ++GYPV++KA+AGGGGKGMR  W+  +  E  
Sbjct: 122 IMEQAGVPLVPGYHGDDQDPAILKQSADNMGYPVLLKATAGGGGKGMRQVWSADEFDEAL 181

Query: 229 RLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEE 288
             + +EA + FGDD MLVEK++  PRH+E+QV CD HGN ++L ER+CS+QRR+QKVIEE
Sbjct: 182 AAAMREAMAGFGDDNMLVEKYLTKPRHVELQVFCDNHGNGVYLAERDCSVQRRHQKVIEE 241

Query: 289 APSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPITE 348
           AP+  +   +R++MG+ AV  A+A+ Y  AGTVEFL+D   +FYF+EMNTRLQVEHP+TE
Sbjct: 242 APAPGMTEALRQRMGDAAVTAARAIDYRGAGTVEFLLDEDGSFYFMEMNTRLQVEHPVTE 301

Query: 349 CITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRYVE 408
            ITG D+V+  L V+ G PLP+TQEQV +NG AFE+RVYAEDP   F LP+ G L     
Sbjct: 302 MITGQDLVRWQLLVASGAPLPLTQEQVRINGHAFEARVYAEDPDNDF-LPATGTLGYLQP 360

Query: 409 PKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTHNI 468
           P     VR D+G+R+G EIS+YYDP+I KL+   +NRE+AL R+  AL  Y I G   N+
Sbjct: 361 PAESRHVRVDTGVRQGDEISVYYDPMIAKLIVWDENRERALQRLASALAEYRIGGTVTNL 420

Query: 469 PLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALNARKLARANQ 528
             L ++   + F   ++ T ++ +     F        ++  + A A  LN ++ A A  
Sbjct: 421 EFLYNLSTSRPFVEAELDTGFIEKHSDLIFHDRHQDLAQELPLAALALLLNKQQNAAAPA 480

Query: 529 FLNQNKQRSTHVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSANKAQVRIGGKTVT 588
             + +   +   + +      V  L V   +   +H+VE   VE   +   VR   K   
Sbjct: 481 NSDSSSPWNDS-SGWRMNEPHVHRLTVHCHQ--ADHSVE---VEQRGDLYLVRAADKDTP 534

Query: 589 ISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLPEQAVKYLQYMKE 648
           + G+L     +  I+ +G  +   +     G    +  G     +V P+          E
Sbjct: 535 LRGELQGEQLL--IDREGHRLRATLAQTHDGFTLYMSDGACHFHEVPPDTG--------E 584

Query: 649 KAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLHAGKTGRVKAVNV 708
                    + +PM G I  + V+P   V+ G  L+VMEAMKM+ ++ A   G V +   
Sbjct: 585 ADGSGTDGGLDAPMNGTIVELLVEPNAQVNTGDALLVMEAMKMEQTIRAPADGTVDSFYY 644

Query: 709 KVGATVDEGEVLV 721
           + G  VD G  L+
Sbjct: 645 QPGDLVDGGAELL 657


Lambda     K      H
   0.316    0.133    0.378 

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: 1144
Number of extensions: 53
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 724
Length of database: 664
Length adjustment: 39
Effective length of query: 685
Effective length of database: 625
Effective search space:   428125
Effective search space used:   428125
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources