GapMind for catabolism of small carbon sources

 

Alignments 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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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