GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Chryseobacterium arthrosphaerae CC-VM-7

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_065401082.1 BBI00_RS22490 3-oxoadipyl-CoA thiolase

Query= SwissProt::P45363
         (394 letters)



>NCBI__GCF_001684965.1:WP_065401082.1
          Length = 401

 Score =  335 bits (858), Expect = 2e-96
 Identities = 185/402 (46%), Positives = 264/402 (65%), Gaps = 12/402 (2%)

Query: 3   DTIVIVDAGRTAIGTFGGALSALQATDIGTTVLKALIERTGIAP-EQVSEVILGQVLTAG 61
           + + I+D  RT I    G LS ++A D+   V+K ++ R    P E++ +VI G    AG
Sbjct: 2   NNVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQAG 61

Query: 62  -CGQNPARQTTLMAGLPHTVPAMTINKVCGSGLKAVHLAMQAVACGDAEIVIAGGQESMS 120
              +N AR   L+AGLP+ +   T+N++C SG+ AV  A +++A G+ EI IAGG E M+
Sbjct: 62  EDNRNVARMGLLLAGLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHMT 121

Query: 121 QSSHVLPRSREGQRMG-DWPMKDT-----MIVDGLWDAFNQCHMGVTAENIAKKYAFTRE 174
           +S +V+  S+ G   G D  M DT      I   + + +    MG TAEN+A  +  +RE
Sbjct: 122 RSPYVM--SKPGAAFGRDSQMFDTTFGWRFINPKMKEMYGVDGMGETAENLADMHHISRE 179

Query: 175 AQDAFAAASQQKAEAAIQSGRFADEIIPVSIPQRKGDPLVFDTDEFPRPGTTAETLGRLR 234
            QD FA  SQQKA  A +SGR A+EI+ V IPQRKG+P++F+ DEF +PG++ E LG+LR
Sbjct: 180 DQDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFEKDEFIKPGSSMEGLGKLR 239

Query: 235 PAFDKQGTVTAGNASGINDGAAMVVVMKESKAKELGLTPMARLVAFSSAGVDPAIMGTGP 294
           PAF K+GTVTAGNASG+NDGAA +++  E   K+ GL P AR++  S AGV+P IMG GP
Sbjct: 240 PAFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRIMGIGP 299

Query: 295 IPASTDCLKKAGWAPADLDLVEANEAFAAQAMSVNQEMGW--DLSKVNVNGGAIAIGHPI 352
           + A+   LK+   +  D+D++E NEAFAAQA++V + +G   D S++N NGGAIAIGHP+
Sbjct: 300 VEATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPL 359

Query: 353 GASGARVLVTLLYEMQKRDAKKGLATLCIGGGQGVALAVERL 394
           G SGAR++ +   E+QK++ K  L TLCIG GQG A+ +E++
Sbjct: 360 GVSGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401


Lambda     K      H
   0.317    0.131    0.380 

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: 321
Number of extensions: 6
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: 394
Length of database: 401
Length adjustment: 31
Effective length of query: 363
Effective length of database: 370
Effective search space:   134310
Effective search space used:   134310
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 (21.7 bits)
S2: 50 (23.9 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