GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Xanthobacter autotrophicus Py2

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_012112924.1 XAUT_RS04530 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-20679
         (395 letters)



>NCBI__GCF_000017645.1:WP_012112924.1
          Length = 402

 Score =  261 bits (668), Expect = 2e-74
 Identities = 177/414 (42%), Positives = 230/414 (55%), Gaps = 32/414 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           M  A I   ARTPIG+ Y GAL       L  H I    +R  G+D + V+DV++G A Q
Sbjct: 1   MAHAFICDFARTPIGR-YAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQ 59

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G    ++AR A L AGLPV+  GTT++R C SGL A+ + AR+++    ++ V GG ES
Sbjct: 60  AGEDNRDVARMAALLAGLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVES 119

Query: 120 IS---LVQNDKMNTFHA-------------VDPALEAIKGDVYMAMLDTAETVAKRYGIS 163
           ++    VQ      F               V+P ++A  G    +M +T E VA+ + +S
Sbjct: 120 MTRAPFVQGKAQEAFSRQAEIYDTTIGWRFVNPLMKAQYG--VDSMPETGENVAEDFQVS 177

Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223
           R  QD ++  SQ+R  AAQ  G F  EIAPI  K        GAV    I +  DE PR 
Sbjct: 178 RADQDLFAYRSQQRVKAAQDAGFFAREIAPIEVK-----GKKGAV----IRVEADEHPRA 228

Query: 224 ETTAEGLAGLKA-VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVS 282
           ETT E LAGLKA  R  G T+TAGNAS ++DGA A ++ S+  A   GL P      +V 
Sbjct: 229 ETTLEQLAGLKAPFRKAGGTVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQ 288

Query: 283 YGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLN 340
            G  P  MGIGP  A  +LL+++GL++ DI L ELNEAFA Q L    +LG+  D E +N
Sbjct: 289 AGVPPRIMGIGPAPATRKLLEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVN 348

Query: 341 VNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
            NGGAI++GHP GMSGARLA  A+     R    AV TMC+G G G A L E V
Sbjct: 349 PNGGAIALGHPLGMSGARLAMTAVSALEVRGGTRAVATMCIGVGQGIAALIERV 402


Lambda     K      H
   0.316    0.134    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: 427
Number of extensions: 30
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: 395
Length of database: 402
Length adjustment: 31
Effective length of query: 364
Effective length of database: 371
Effective search space:   135044
Effective search space used:   135044
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: 50 (23.9 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