GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Methylocystis bryophila S285

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_085770214.1 B1812_RS02620 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_002117405.1:WP_085770214.1
          Length = 391

 Score =  242 bits (618), Expect = 1e-68
 Identities = 154/398 (38%), Positives = 220/398 (55%), Gaps = 25/398 (6%)

Query: 2   TEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQG 61
           T+ VIVS ART +G ++ GA        L   A++ A++RA + P EV +V++G  +   
Sbjct: 3   TDIVIVSAARTAVG-SFNGAFGGVPAHELGAAAVKSALERAKVAPSEVCEVILGQVLG-A 60

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
           A G N AR+A ++AG+P +     I++ C SGL+A+ALAA+ +     +I V GG ES+S
Sbjct: 61  AQGQNPARQAAIKAGVPDSATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQESMS 120

Query: 122 LVQN-------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEYSL 172
           L  +        KM      D  +     D +    M  TAE VA ++ ISR  QD +++
Sbjct: 121 LSTHAAHMRAGTKMGPVSFADTMIIDGLTDAFNNYHMGITAENVAAKWQISRAEQDAFAV 180

Query: 173 ESQRRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230
            SQ +  AAQ+ GKF DEI P  IST+ G            D+ +  DE  +   T E +
Sbjct: 181 ASQNKAEAAQKAGKFKDEILPYTISTRKG------------DVVVDSDEYVKHGVTLESV 228

Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290
           + L+    +  T+TA NAS L+DGA+A V+MS   A  +GL+PL       + G +P  M
Sbjct: 229 SKLRPAFTKDGTVTAANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIM 288

Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350
           G GP+ A  + L++ G  V D+ L E NEAFA Q +     LG DP  +NVNGGAI++GH
Sbjct: 289 GSGPIPATRKALEKAGWKVSDLNLVEANEAFAAQAIAVNKDLGWDPAIVNVNGGAIAIGH 348

Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           P G SGAR+    L E +RR     + T+C+GGGMG A
Sbjct: 349 PIGASGARILTTLLYELKRRGGGKGLATLCIGGGMGIA 386


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: 447
Number of extensions: 21
Number of successful extensions: 4
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: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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