Aligments for a candidate for pccB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccB in Acidovorax sp. GW101-3H11

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_1923 Geranyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.5)

Query= metacyc::MONOMER-17283
         (535 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1923
          Length = 537

 Score =  413 bits (1061), Expect = e-119
 Identities = 240/543 (44%), Positives = 322/543 (59%), Gaps = 17/543 (3%)

Query: 2   SIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRID 61
           ++  S   P S +     A  Q+    LR  L +      A    + E+RG+L  R R+ 
Sbjct: 3   AVFTSRFNPGSAEATQRRAALQARLDALRA-LEERAAAASARSLPQFEKRGQLLPRQRVA 61

Query: 62  TLIDPDSSFLEIGALAAY--NVYDEE--VPAAGIVCGIGRVAGRPVMIIANDATVKGGTY 117
            L+D  + +L +  LA Y  +V D E  VP  G+V GIG V+G   M++A+D+ ++ G  
Sbjct: 62  LLLDAGAPWLPLCTLAGYLQDVKDPEKSVPGGGMVAGIGFVSGVRCMVVASDSGIEAGAI 121

Query: 118 FPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLP-LQSEVFPDRDHFGRIFYNQAQMSAE 176
            P+ ++K LR QEIA +NRLP I+LV+S GA L   + E F    H G +F N A++SA 
Sbjct: 122 QPMGLEKILRVQEIALQNRLPFIHLVESAGANLMRYRVEGFV---HGGTLFRNLARLSAA 178

Query: 177 GIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGAD 236
           GIP I    GS TAGGAY+P +SD V++V+G    FL GPPL+KAATGE  T EELGGA+
Sbjct: 179 GIPVITVQHGSGTAGGAYMPGLSDVVIMVQGRSRAFLAGPPLLKAATGEIATEEELGGAE 238

Query: 237 VHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEP-PRYDPREIYGILPR 295
           +HT +SG+ +Y A DDREA+ + RD+VA LG     N   R   P P     ++  ++  
Sbjct: 239 MHTAVSGLGEYLAQDDREAIGLARDVVAQLG----WNMPRRPSAPVPLLPADDLLSLMSA 294

Query: 296 DFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALK 355
           D RQ  D+REV+AR+VDGS L EFK RYG   VC   HI G  VG ++NNG +    A K
Sbjct: 295 DLRQPVDMREVMARLVDGSELLEFKARYGMATVCAQGHIGGHAVGFISNNGPIDVAGANK 354

Query: 356 GAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGG 415
             HFI+  C    P+++LQN TG+MVGK  E GG+ K G+K++ AV+ A VP+ T+  G 
Sbjct: 355 ATHFIQWMCQLGHPIIYLQNTTGYMVGKDSEQGGMIKHGSKMIQAVTNATVPQITIQCGA 414

Query: 416 SFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQE 475
           SFGAGNYGMCGR Y PR L+ WP A+ +VMGG QAA  +  +    L  +G    P E +
Sbjct: 415 SFGAGNYGMCGRGYAPRFLFSWPGAKTAVMGGEQAARTMQIVTEAALARKGITPDPAESQ 474

Query: 476 RFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPTRFGV 532
                I+A +E +   +Y S  L DDGVIDP +TR VLA  L   AEA    ++P  FGV
Sbjct: 475 AQFDKIVAMFEAQADVFYTSGLLLDDGVIDPRDTRAVLAFCLDTCAEAQARTLRPLSFGV 534

Query: 533 FRM 535
            RM
Sbjct: 535 ARM 537


Lambda     K      H
   0.322    0.139    0.423 

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: 731
Number of extensions: 37
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: 535
Length of database: 537
Length adjustment: 35
Effective length of query: 500
Effective length of database: 502
Effective search space:   251000
Effective search space used:   251000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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 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

GapMind for catabolism of small carbon sources