GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Amycolatopsis halophila YIM 93223

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_034270164.1 AMYHA_RS09575 methylcrotonoyl-CoA carboxylase

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



>NCBI__GCF_000504245.1:WP_034270164.1
          Length = 537

 Score =  743 bits (1919), Expect = 0.0
 Identities = 364/532 (68%), Positives = 418/532 (78%)

Query: 4   IHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63
           + S   P S DFQ   A H  L ADL  R+ Q   GG  + R RH ERGKL  RDR+D L
Sbjct: 6   LRSDADPASEDFQRYAAEHGQLVADLNGRVKQAMHGGPEKSRVRHVERGKLLPRDRVDAL 65

Query: 64  IDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVK 123
           +DP S FLE+  LAA  +YD+E PAAGI+ G+GRV+GR  +I+ANDATVKGGTY+P+TVK
Sbjct: 66  LDPGSPFLELSPLAANGMYDDEAPAAGIITGVGRVSGRECVIVANDATVKGGTYYPITVK 125

Query: 124 KHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIAC 183
           KHLRAQE+A  N LPC+YLVDSGGA+LP Q  VFPDR+HFGRIFYNQA MSA GIPQIA 
Sbjct: 126 KHLRAQEVALHNNLPCVYLVDSGGAFLPEQDGVFPDREHFGRIFYNQATMSARGIPQIAA 185

Query: 184 VMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISG 243
           V+GSCTAGGAYVPAMSDE VIV+  GTIFLGGPPLVKAATGEEVT EELGG DVH R SG
Sbjct: 186 VLGSCTAGGAYVPAMSDEAVIVRNQGTIFLGGPPLVKAATGEEVTDEELGGGDVHARQSG 245

Query: 244 VADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDV 303
           V D+ ANDD +AL IVR IV+ LGPR    W++   E P  DP E+YG++P D R  YDV
Sbjct: 246 VTDHLANDDTDALRIVRSIVSTLGPRVPRPWDVAPVEEPAVDPTELYGVVPTDSRTPYDV 305

Query: 304 REVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELC 363
           REVIAR+VDGSR  EFK  YGTTLV GFA I G PVGI+ANNG+LF+ESA+KGAHFIELC
Sbjct: 306 REVIARVVDGSRFAEFKAEYGTTLVTGFARIHGHPVGIIANNGVLFAESAMKGAHFIELC 365

Query: 364 CARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYG 423
             R+IPL+FLQNITGFMVGK YE GGIAK GAK+VTAV+CA VPK TVIIGGSFGAGNY 
Sbjct: 366 DKRSIPLLFLQNITGFMVGKDYEAGGIAKHGAKMVTAVACARVPKLTVIIGGSFGAGNYS 425

Query: 424 MCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILA 483
           MCGRAY PR LWMWPNARISVMGG QAA+VL T+RRD +  RG+  + E++E F  PI  
Sbjct: 426 MCGRAYSPRFLWMWPNARISVMGGEQAASVLSTVRRDAIERRGETWSAEDEEAFKDPIRE 485

Query: 484 KYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           +YE +GHPYY++ARLWDDGVIDPV+TR V+ L L+AAA AP+    +GVFRM
Sbjct: 486 QYEHQGHPYYSTARLWDDGVIDPVDTRTVVGLALSAAANAPLDDISYGVFRM 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: 985
Number of extensions: 42
Number of successful extensions: 2
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 24 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